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R/MiRNANameConverter.R
In miRNAmeConverter: Convert miRNA Names to Different miRBase Versions
Defines functions
.check
#' @title MiRNANameConverter constructor
#'
#' @description This function returns an instance of a MiRNANAmeConverter class.
#' Handling mature miRNA names from different miRBase versions
#' This package contains algorithms for dealing with mature miRNA names
#' from different miRBase release versions. The functions are provided in form
#' of methods as part of the \code{MiRNANameConverter}-class. The data of all
#' the miRBase release versions is stored in the \code{miRBaseVersions.db}
#' annotation package.
#' The \emph{MiRNAmeConverter} package contains one class that has two
#' categories of functions: getters-functions and algorithms.
#' @seealso \emph{miRBaseVersions.db} for more information about the
#' database holding all major miRBase release versions)
#'
#' @section Classes:
#' The \code{MiRNANameConverter}
# class is an S4 class that provides all the
# functions that are needed for dealing with challenges introduced over
# different miRBase releases.
#' @section Getter functions:
#' The getter functions provide access to the slots of the class.
#' @section Algorithms:
#' There are three algorithms for dealing with miRNA names from different
#' miRBase releases, the \code{\link{assessVersion}},
#' \code{\link{checkMiRNAName}} and \code{\link{translateMiRNAName}}.
#' \describe{
#' \item{\code{\link{translateMiRNAName}}}{The algorithm coded in this
#' function can translate given miRNA names to different
#' miRBase release versions.}
#' \item{\code{\link{checkMiRNAName}}}{This function is used to check if a
#' given miRNA name is listed in the current miRBase release.}
#' \item{\code{\link{assessVersion}}}{The \emph{assessVersion}}-function is
#' useful when one wants to assess the miRBase version of a given set
#' of mature miRNA names.
#' }
#'
#' @docType package
#' @name miRNAmeConverter
#'
#' @author Stefan Haunsberger \email{stefanhaunsberger@rcsi.ie}
#' @examples
#' # Translate a mature miRNA name to miRBase version 21.0
#' nc = MiRNANameConverter(); # Object instantiation
#' translateMiRNAName(nc, "hsa-miR-29a", version = 21.0)
#' @import DBI miRBaseVersions.db AnnotationDbi reshape2
NULL
# source("R/tools/printFunctionEntryInformation.R");
# source("R/tools/printFunctionExitInformation.R");
# Add package specific environment
# pkg.env <- new.env();
#' @title Instantiate from MiRNANameConverter class
#'
#' @description This function returns back an instance of a
#' \emph{MiRNANAmeConverter} object.
#'
#' @slot .dbconn Database connection
#' @slot .currentVersion Current miRBase version
#' @slot .validVersions Valid/Supported miRBase versions
#' @slot .nOrganisms Number of different organisms supported
#' @slot .nTotalEntries Total number of mature miRNA names among all provided
#' miRBase release versions in the \emph{miRBaseVersions.db} package.
#' @slot .validOrganisms Valid organisms
#' @author Stefan Haunsberger
#'
# @param this Object of class \code{MiRNANameConverter}
#' @param ... any optional arguments
MiRNANameConverter = setClass(
# Set the name for the class
Class = "MiRNANameConverter",
# Define the slots
slots = representation(
.dbconn = "SQLiteConnection",
.currentVersion = "numeric",
.validVersions = "numeric",
.nOrganisms = "integer",
.nTotalEntries = "integer",
.validOrganisms = "character"
),
# Set the default values for the slots. (optional)
prototype = list(
.dbconn = NULL,
.currentVersion = NULL,
.validVersions = NULL,
.nOrganisms = NULL,
.nTotalEntries = NULL,
.validOrganisms = NULL
)
)
##### initialization ####
# Initialization function (constructor)
setMethod(
f = "initialize",
signature("MiRNANameConverter"),
definition = function(.Object) {
# writeLines("MiRNANameConverter-constructor");
# library(miRBaseVersions.db);
args = as.list(match.call());
# Store database connection
.dbconn(.Object) = AnnotationDbi::dbconn(miRBaseVersions.db);
con = .dbconn(.Object);
# Recive all version numbers from the db
versions = (DBI::dbGetQuery(con,
"SELECT number AS version FROM version;"))$version;
validVersions(.Object) = versions;
currentVersion(.Object) = as.numeric(
AnnotationDbi::dbmeta(con,
"current_version"));
nOrganisms(.Object) =
DBI::dbGetQuery(con,
"SELECT count(DISTINCT organism) as n FROM mimat")$n;
nTotalEntries(.Object) =
DBI::dbGetQuery(con,
"SELECT count(*) as n FROM mimat")$n;
validOrganisms(.Object) =
DBI::dbGetQuery(con,
"SELECT organism FROM organism")$organism;
return(.Object);
}
)
#'
#'
.check = function(input) {
# Correct 'mir-' with 'miR-'
# output = gsub("mir-", "miR-", input, ignore.case = TRUE);
# Remove quotations (single and double)
output = gsub("\"|\'|--", "", input);
return(output);
}
##### MiRNANameConverter - constructor ####
#' @title MiRNANameConverter constructor
#'
#' @description This function returns an instance of a MiRNANAmeConverter class.
#'
#' @return an object of class 'MiRNANameConverter'
#' @examples
#' nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
#'
#' @details
#' This function initializes an object of the class MiRNANameConverter. It is a
#' wrapper for \code{new()}.
#'
#' @seealso \code{\link{new}}
#' @author Stefan Haunsberger
#' @export MiRNANameConverter
setMethod(
f = "MiRNANameConverter",
signature(),
definition = function() {
return(new('MiRNANameConverter'));
}
)
##### checkMiRNAName ####
#' @title Check miRNA names for validity
#'
#' @description This function checks for a given set of mature 'miRNAs' (names)
#' Check miRNA names for validity
#'
#' This function checks for a given set of mature 'miRNAs' (names)
#' if the names are listed in any miRBase version respectively.
#'
#' @details
#' This function takes the input miRNA names and checks each one of them for
#' validity. The check is done by taking each miRNA and searches for an existing
#' entry in the miRBase database among all versions. miRNAs that are listed in
#' any version will be comprised in the return vector respectively. If no valid
#' miRNA was detected, a \code{character(0)} will be returned.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param verbose A boolean to either show more (TRUE) or less
#' information (FALSE)
#' @return A character vector containing a set of valid miRNA names
#'
#' @examples
#' nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
#' # Test with correct inputs
#' checkMiRNAName(nc, miRNAs = c("hsa-miR-29a", "hsa-miR-642"))
#'
#' @importFrom DBI dbGetQuery
#' @author Stefan Haunsberger
#' @rdname checkMiRNAName
#' @export
setGeneric(
name = "checkMiRNAName",
def = function(this,
miRNAs,
verbose = FALSE) {
standardGeneric("checkMiRNAName");
}
)
#' @describeIn checkMiRNAName Method for checking for valid miRNA names
setMethod(
f = "checkMiRNAName",
signature("MiRNANameConverter"),
definition = function(this,
miRNAs,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'...
.\nPlease try again with a valid class.",
class(miRNAs)));
}
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
# Check which entries are acutally miRNAs listed in the miRBase repository
miRNAs.valid = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT name FROM 'vw-mimat-mirna-unique'
WHERE UPPER(name) IN (\"%s\")
ORDER BY name ASC",
paste(toupper(miRNAs.unique),
collapse = "\", \""))))$name;
n.miRNAs.valid = length(miRNAs.valid);
if (n.miRNAs.valid != length(miRNAs.unique)) {
miRNAs.invalid = miRNAs.unique[!(toupper(miRNAs.unique)
%in%
toupper(miRNAs.valid))];
if (length(miRNAs.invalid) == 1) {
message("\tThe following miRNA is not listed in the miRBase repository:");
} else {
message("\tThe following miRNAs are not listed in the miRBase repository:");
}
message(paste0(miRNAs.invalid, collapse = "; "));
}
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
# if (correct) {
# return(miRNAs.valid);
# } else {
return(miRNAs.unique[(toupper(miRNAs.unique)
%in%
toupper(miRNAs.valid))])
# }
}
)
##### assessMiRNASwappingMIMAT ####
#' @title Check if given miRNA names can be assigned to unique MIMAT
#' accessions among all versions
#'
#' @description This function checks if the names from a given set of mature
#' miRNAs have a unique MIMAT ID.
#' Check if given miRNA names can be assigned to unique MIMAT accessions among
#' all versions
#'
#' This function checks if the names from a given set of mature miRNAs
#' have a unique MIMAT ID.
#'
#' @details
#' Although the majority of miRNA names can be assigned to a unique MIMAT ID
#' (accession) some miRNAs changed MIMAT ID in different versions. This function
#' takes the input miRNA names and checks each one of them if they have a unique
#' MIMAT ID over all versions. If a miRNA changes MIMAT ID in a version it will
#' be comprised in the return vector.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param verbose A boolean to either show more (TRUE) or less information
#' (FALSE)
#' @return A character vector containing miRNA names that do not have a unique
#' MIMAT ID
#'
#' @author Stefan Haunsberger
#'
# @export
#' @rdname assessMiRNASwappingMIMAT
setGeneric(
name = "assessMiRNASwappingMIMAT",
def = function(this,
miRNAs,
verbose = FALSE) {
standardGeneric("assessMiRNASwappingMIMAT");
}
)
# @describeIn assessMiRNASwappingMIMAT Method for assessing miRNA names that
# swapped MIMAT-accession
setMethod(
f = "assessMiRNASwappingMIMAT",
signature("MiRNANameConverter"),
definition = function(this,
miRNAs,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'.\nPlease try again with a valid class.", class(miRNAs)));
}
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
# Check which entries are acutally miRNAs listed in the miRBase repository
miRNAs.swapped = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT name FROM 'vw-mimat-mirna-swapped-mimat'
WHERE UPPER(name) IN (\"%s\")
ORDER BY name ASC",
paste(toupper(miRNAs.unique), collapse = "\", \""))))$name;
n.miRNAs.swapped = length(miRNAs.swapped);
if (n.miRNAs.swapped == 1) {
message("\tFollowing miRNA does not have a unique MIMAT accession among the versions:");
message(paste0(miRNAs.swapped, collapse = "; "));
} else if (n.miRNAs.swapped > 1){
message("\tFollowing miRNAs do not have a unique MIMAT accession among the versions:");
message(paste0(miRNAs.swapped, collapse = "; "));
}
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
return(miRNAs.swapped);
}
)
##### assessVersion ####
#' @title Assess miRBase version
#'
#' @description This function detects the most likely miRBase version of a
#' given miRNA set.
#' Assess miRBase version
#'
#' This function detects the most likely miRBase version of a given miRNA set.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param verbose A boolean to either show more (TRUE) or less information (FALSE)
#' @return A data frame with two columns: version and frequency (decreasing
#' order by frequency, version)
#' + version: miRBase version
#' + frequency: the number of valid miRNAs that could be assigned
#' to the version respectively
#'
#' @examples
#' nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
#' assessVersion(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"))
#'
#' @details
#' This function takes a set of miRNA names and detects the most likely miRBase
#' version of this given set of 'miRNAs'. First all miRNAs will be checked for
#' validity (if they are actual miRNA names \code{checkMiRNAName} and the set
#' that passes the check will be further processed.
#'
#' @author Stefan Haunsberger
#' @rdname assessVersion
#' @export
setGeneric(
name = "assessVersion",
def = function(this,
miRNAs,
verbose = FALSE) {
standardGeneric("assessVersion");
}
)
#' @describeIn assessVersion Method for assessing the most likely miRBase
#' version that a given set of miRNA names is from.
setMethod(
f = "assessVersion",
signature("MiRNANameConverter"),
definition = function(this,
miRNAs,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'.\nPlease try again with a valid class.", class(miRNAs)));
}
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
# Check which entries are acutally miRNAs listed in the miRBase repository
miRNAs.valid = checkMiRNAName(this, miRNAs.unique);
n.miRNAs.valid = length(miRNAs.valid);
# Receive miRBase versions with number of assigned miRNAs
versions = DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT version, count(*) as frequency FROM mimat
WHERE UPPER(name) IN (\"%s\")
GROUP BY version
ORDER BY frequency DESC, version DESC;",
paste(toupper(miRNAs.valid), collapse = "\", \"")));
version = versions$version[1];
# Check which miRNAs could not be assigned to the identified version
n.miRNAs.not.version = 0;
if (n.miRNAs.valid != versions$frequency[1]) {
miRNAs.version = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT name FROM 'vw-mimat-%2.1f'
WHERE UPPER(name) IN (\"%s\")",
version, paste(toupper(miRNAs.valid),
collapse = "\", \""))))$name;
miRNAs.not.version = miRNAs.valid[!(toupper(miRNAs.valid)
%in%
toupper(miRNAs.version))];
n.miRNAs.not.version = length(miRNAs.not.version);
if (n.miRNAs.not.version == 1) {
message(sprintf("\tmiRNA that could not be found in identified max version %2.1f:", version));
} else {
message(sprintf("\tmiRNAs that could not be found in identified max version %2.1f:", version));
}
message(paste0(miRNAs.not.version, collapse = "; "));
}
message(sprintf("-> %i out of %i valid miRNAs assigned to max version %2.1f.", versions$frequency[1], n.miRNAs.valid, version));
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
return(versions);
}
)
##### translateMiRNAName ####
#' @title Translate miRNA name
#'
#' @description This function translates input miRNA names to different
#' miRBase versions.
#' Translate miRNA name
#'
#' This function translates input miRNA names to different miRBase versions.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param versions An integer or numerical vector containing the target versions
#' @param sequenceFormat Integer value indicating the return format for the
#' data frame containing sequence information
#' {1=only sequences, 2=miRNA name and sequence}
#' @param verbose A boolean to either show more (TRUE) or less information
#' (FALSE)
#' @return A (n x m) data frame where n is the number of valid miRNAs and m the
#' number of
#' columns (minimum 3 columns, MIMAT-ID (accession), input miRNA name, current
#' version)
#' In addition an attribute 'description' is added to the data frame where to
#' each miRNA some notes are added (for example why a certain miRNA is not
#' in the output).
#' Sequence information is attached as the attribute 'sequence'.
#'
#' @examples
#' nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
#' res = translateMiRNAName(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"),
#' versions = c(15, 16, 20, 21))
#' res
#' attributes(res)
#' @seealso \code{\link{attr}} for attributes
#'
#' @details
#' The translation and sequence retrieval are done in 5 main steps:
#' 1) Only take miRNA names that do not swap MIMAT IDs among versions
#' (\code{\link{assessMiRNASwappingMIMAT}})
#' 2) Check, if the miRNA names are valid names (\code{\link{checkMiRNAName}})
#' 3) Receive unique MIMAT IDs for each valid miRNA
#' - If there are miRNAs that have basically the same name,
#' only use miRNA names from the highest version
#' 4) Check if the found MIMAT IDs are still listed in the
#' current miRBase version
#' - If not, neglect it because then it is not considered to be a
#' miRNA anymore
#' 5) Receive names from desired versions
#'
#' @author Stefan Haunsberger
#' @rdname translateMiRNAName
#' @export
setGeneric(
name = "translateMiRNAName",
def = function(this,
miRNAs,
versions,
sequenceFormat = 1,
verbose = FALSE) {
standardGeneric("translateMiRNAName");
}
)
#' @describeIn translateMiRNAName Method for translating miRNA name(s) to
#' different miRBase versions
setMethod(
f = "translateMiRNAName",
signature(this = "MiRNANameConverter", miRNAs = "character"),
definition = function(this,
miRNAs,
versions,
sequenceFormat,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'.\nPlease try again with a valid class.", class(miRNAs)));
}
# Substitute characters/clean
miRNAs = .check(miRNAs);
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
if (is.null(args$versions)) {
versions = this@.currentVersion;
} else {
if (!all(versions %in% this@.validVersions)) {
message(sprintf("Argument 'versions' is not valid."));
message("Valid versions are:");
message(sprintf("%2.1f", this@.validVersions));
stop("Please try again with valid 'versions' argument.");
} else {
versions = unique(versions);
}
}
# Initialize data frame with description to each miRNA
description = data.frame(input.miRNA = miRNAs.unique,
information = "OK",
stringsAsFactors = FALSE,
row.names = miRNAs.unique);
###### ### ###
# 1) Check for MIMAT swapping miRNAs
## Only use miRNAs that are not swapping MIMATs as input
miRNAs.swapping = suppressMessages(
assessMiRNASwappingMIMAT(
this,
miRNAs.unique, verbose = verbose
)
);
miRNAs.not.swapping = miRNAs.unique[!(miRNAs.unique %in% miRNAs.swapping)];
if (length(miRNAs.swapping) > 0) {
if (length(miRNAs.swapping) == 1) {
message("\tFollowing miRNA will be neglected due to non unique MIMAT accession:");
} else {
message("\tFollowing miRNAs will be neglected due to non unique MIMAT accession:");
}
message(paste0(miRNAs.swapping, collapse = "; "));
}
description[miRNAs.swapping, "information"] = "This miRNA does not have a unique MIMAT ID.";
if (length(miRNAs.not.swapping) == 0) {
message("No further miRNAs to process, return NULL.");
return(NULL);
}
###### ### ###
# 2) Check which entries are acutally miRNAs listed in the miRBase repository
## Only process miRNAs that are valid miRNA names
miRNAs.valid = suppressMessages(checkMiRNAName(this,
miRNAs.not.swapping,
verbose = verbose));
miRNAs.not.valid = miRNAs.not.swapping[!(toupper(miRNAs.not.swapping)
%in% toupper(miRNAs.valid))];
n.miRNAs.valid = length(miRNAs.valid);
n.miRNAs.dif = length(miRNAs.not.swapping) - n.miRNAs.valid;
# print(miRNAs.valid)
miRNAs.valid = suppressMessages(
checkMiRNAName(
this
,miRNAs.not.swapping
,verbose = verbose
)
);
miRNAs.not.valid = miRNAs.not.swapping[!(toupper(miRNAs.not.swapping)
%in% toupper(miRNAs.valid))];
n.miRNAs.valid = length(miRNAs.valid);
n.miRNAs.dif = length(miRNAs.not.swapping) - n.miRNAs.valid;
if (length(miRNAs.valid) == 0) {
message("No valid miRNAs found.");
return(NULL);
}
if (n.miRNAs.dif != 0) {
if (n.miRNAs.dif == 1) {
message("\tFollowing miRNA will be neglected (not listed in miRBase):");
} else {
message("\tFollowing miRNAs will be neglected (not listed in miRBase):");
}
message(paste0(miRNAs.not.valid, collapse = "; "));
}
description[miRNAs.not.valid, "information"] =
"This name is not listed in any miRBase version.";
###### ### ###
# 3) Check if there are miRNAs that have the same name -> same MIMAT
## name accession version
## e.g.: 2 hsa-let-7a* MIMAT0004481 17
## 3 hsa-let-7a-3p MIMAT0004481 21 --> would be chosen
## They are basically the same but input names are from different versions
## Receive unique MIMAT accessions for each miRNA name with the
## maximum version number
mimats.versions = DBI::dbGetQuery(
conn = .dbconn(this)
,sprintf("SELECT DISTINCT accession, name,
MAX(version) as version FROM mimat
WHERE UPPER(name) IN (\"%s\")
GROUP BY accession, name
ORDER BY accession",
paste(toupper(miRNAs.valid),
collapse = "\", \"")
)
);
if (length(miRNAs.valid) == 1) {
mimats = mimats.versions$accession;
names = mimats.versions$name;
} else {
mimats.versions.split = split(mimats.versions,
mimats.versions$accession);
mimats = character(length(unique(mimats.versions$accession)));
names = character(length(unique(mimats.versions$accession)));
for (i in 1:length(mimats.versions.split)) {
idx = 1;
if (nrow(mimats.versions.split[[i]]) > 1) {
# Take the name from the highest version
idx = which.max((mimats.versions.split[[i]])$version);
name = mimats.versions.split[[i]]$name[idx];
name.other = mimats.versions.split[[i]]$name[-idx];
writeLines(sprintf("\tmiRNA '%s' is the same as '%s'.",
name, paste(name.other, collapse = ", ")));
writeLines(sprintf("\t->%s is the most recent one and will be used. The other ones will be neglected.", name));
# Add description to miRNAs that will be neglected
description[name.other, "information"] =
sprintf("This miRNA is the same as input miRNA name '%s' from version %2.1f.",
name, (mimats.versions.split[[i]])$version[idx]);
}
mimats[i] = mimats.versions.split[[i]]$accession[idx];
names[i] = mimats.versions.split[[i]]$name[idx];
}
}
###### ### ###
# 4) Check which MIMATs are listed in the current miRBase release
## Only take miRNAs that are listed in the current version
### Receive mimats that are listed in the current version
mimats.current = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
this@.currentVersion, paste(toupper(mimats),
collapse = "\", \""))))$accession;
mimats.invalid = mimats[!(mimats %in% mimats.current)];
names.invalid = names[!(mimats %in% mimats.current)];
if (length(mimats.invalid) > 0) {
if (length(mimats.invalid) == 1) {
message(sprintf("\tFollowing miRNA is not listed in the current miRBase version %2.1f.",
this@.currentVersion));
} else {
message(sprintf("\tFollowing miRNAs are not listed in the current miRBase version %2.1f.",
this@.currentVersion));
}
message(paste0(names.invalid, collapse = "; "));
}
### Exclude MIMATs that are not listed in the current version
mimats.valid = mimats[mimats %in% mimats.current];
names.valid = names[mimats %in% mimats.current];
description[names.invalid, "information"] =
sprintf("This miRNA is not listed in the current miRBase version %2.1f.",
this@.currentVersion);
###### ### ###
# 5) Translate miRNA names to desired versions
## Initialize return data frame for miRNA names and sequences
### miRNA names
## Initialize return data frame
n.col = 2 + length(versions);
headers = c("mimat", "input",
paste0("v", sprintf("%2.1f",versions)));
df = as.data.frame(matrix(data = NA_character_, nrow =
length(mimats.valid), ncol = n.col));
colnames(df) = headers;
### Sequences
if (sequenceFormat == 1) {
dfSeq = as.data.frame(matrix(data = NA_character_,
nrow = length(mimats.valid),
ncol = n.col),
stringsAsFactors = FALSE);
colnames(dfSeq) = c("mimat", "input",
paste0("v", sprintf("%2.1f",versions)));
} else {
dfSeq = as.data.frame(matrix(data = NA_character_,
nrow = length(mimats.valid),
ncol = 2 + 2 * length(versions)),
stringsAsFactors = FALSE);
nam = unlist(
lapply(paste0("v", sprintf("%2.1f",versions)),
function(y1) {
lapply(c("miRNA", "Sequence"),
function(y2) {
paste(y1, y2, sep="-")
})}));
colnames(dfSeq) = c("mimat", "input", nam);
rm(nam);
}
# Convert factor columns to character columns
fac.cols = sapply(df, is.factor);
df[, fac.cols] = sapply(df[, fac.cols], as.character);
# colnames(df) = headers;
fac.cols = sapply(dfSeq, is.factor);
dfSeq[, fac.cols] = sapply(dfSeq[, fac.cols], as.character);
# colnames(dfSeq) = headers;
df$mimat = mimats.valid;
df$input = names.valid;
dfSeq$mimat = mimats.valid;
dfSeq$input = names.valid;
rownames(df) = mimats.valid;
rownames(dfSeq) = mimats.valid;
## Iterate over desired versions and
for (version in versions) {
miRNAs.version =
DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession, name FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
version, paste(toupper(df$mimat),
collapse = "\", \"")));
df[miRNAs.version$accession,
sprintf("v%2.1f",version)] = miRNAs.version$name;
# sequences
if (sequenceFormat == 1) {
# Only accession and sequence
seq.version = DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession, sequence
FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
version, paste(toupper(df$mimat),
collapse = "\", \"")));
dfSeq[seq.version$accession,
sprintf("v%2.1f",version)] = seq.version$sequence;
} else {
# Accession, miRNA name and sequence
seq.version = DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession, name, sequence
FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
version, paste(toupper(df$mimat),
collapse = "\", \"")));
dfSeq[seq.version$accession,
sprintf("v%2.1f-Sequence",version)] = seq.version$sequence;
dfSeq[miRNAs.version$accession,
sprintf("v%2.1f-miRNA",version)] = miRNAs.version$name;
}
}
# Reorder data frames
## df by MIMAT ID
## description by input miRNA names
df = df[order(df$mimat),];
dfSeq = dfSeq[order(dfSeq$mimat),];
description = description[order(description$input.miRNA),];
# Add description as an attribute
attr(df, "description") = description;
attr(df, "sequence") = dfSeq;
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
return(df);
})
##### saveResults ####
#' @title Save miRNA translation results
#'
#' @description This function saves the data frame returned from
#' translateMiRNAName inclusive the attribute 'description'.
#' Save miRNA translation results
#'
#' This function saves the data frame returned from translateMiRNAName
#' inclusive the attribute 'description'.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param df A \code{data.frame} with translated results
#' @param outputFilename A filename for the output file, such as 'filename.txt'
#' @param outputPath A file path (character string) to the target directory
#' @param sep Separator
#' @param quote If all data values shall be surrounded by ('"')
#' @param verbose Boolean to either show more (TRUE) or less information (FALSE)
#' @param ... Arguments that can be passed on to \code{write.table}
#'
#' @examples
#' nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
#' res = translateMiRNAName(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"),
#' versions = c(15, 16, 20, 21))
#' # Save translation results
#' saveResults(nc, res)
#'
#' @details
#' This function saves a data frame that has been returned by
#' \code{translateMiRNAName}.
#' The attribute 'description' of the data frame will be stored as well.
#'
#' @seealso \code{\link{write.table}} for additional parameter values for
#' the '...' argument, \code{\link{attr}} for how to retrieve attributes
#' @author Stefan Haunsberger
#' @rdname saveResults
#' @export
setGeneric(
name = "saveResults",
def = function(this,
df,
outputFilename,
outputPath,
sep = "\t",
quote = FALSE,
verbose = FALSE,
...) {
standardGeneric("saveResults");
}
)
#' @describeIn saveResults Method for saving translation results
setMethod(
f = "saveResults",
signature(this = "MiRNANameConverter", df = "data.frame"),
definition = function(this,
df,
outputFilename,
outputPath,
sep,
quote,
verbose,
...) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (is.null(args$outputFilename)) {
time = format(Sys.time(), "%H%M%S");
date = format(Sys.Date(), "%d%m%Y");
outputFilename = sprintf("miRNA-name-translation-%s-%s.txt",
date, time);
}
if (is.null(args$outputPath)) {
outputPath = ".";
} else {
if (!file.exists(outputPath)) {
message(sprintf("Given outputPath '%s' does not exist.",
outputPath));
stop("Please try again with valid output path.");
}
}
# Construct 'file' (path incl. filename, such as <path>/filename.txt)
output.file = file.path(outputPath, outputFilename);
if (file.exists(output.file)) {
prefix = substr(outputFilename, 1,
sapply(gregexpr("\\.", outputFilename), tail, 1) - 1);
suffix = substr(outputFilename,
sapply(gregexpr("\\.", outputFilename), tail, 1),
nchar(outputFilename));
time = gsub(pattern = ":", replacement = "", x = (format(Sys.time(), "%X")));
date = format(Sys.Date(), "%d-%m-%Y");
outputFilename = sprintf("%s-%s-%s%s", prefix, date, time, suffix);
message(sprintf("Output file already exists -> Save file under name '%s'", outputFilename));
output.file = file.path(outputPath, outputFilename);
}
writeLines(sprintf("\tSave file to '%s'...", output.file));
utils::write.table(df, file = output.file, row.names = FALSE, quote = FALSE, sep = sep);
# description
if (!is.null(attributes(df)$description)) {
prefix = substr(outputFilename, 1,
sapply(gregexpr("\\.", outputFilename), tail, 1) - 1);
suffix = substr(outputFilename,
sapply(gregexpr("\\.", outputFilename), tail, 1),
nchar(outputFilename));
outputFilenameDesc = sprintf("%s-description%s", prefix, suffix);
output.file = file.path(outputPath, outputFilenameDesc);
writeLines(sprintf("\tSave file to '%s'...", output.file));
utils::write.table(attributes(df)$description, file = output.file,
row.names = FALSE, quote = FALSE, sep = sep);
}
if (!is.null(attributes(df)$sequence)) {
prefix = substr(outputFilename, 1,
sapply(gregexpr("\\.", outputFilename), tail, 1) - 1);
suffix = substr(outputFilename,
sapply(gregexpr("\\.", outputFilename), tail, 1),
nchar(outputFilename));
outputFilenameSeq = sprintf("%s-sequence%s", prefix, suffix);
output.file = file.path(outputPath, outputFilenameSeq);
writeLines(sprintf("\tSave file to '%s'...", output.file));
utils::write.table(attributes(df)$sequence, file = output.file,
row.names = FALSE, quote = FALSE, sep = sep);
}
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
invisible(return);
})
##### show ####
#' @title Show-method
#'
#' @description This function prints object specific information
#' Show-method
#'
#' This function prints object specific information
#'
#' @details
#' This function prints some information to the console.
#' @param object Object of class \code{MiRNANameConverter}
#' @seealso \code{\link{show}}
#'
#' @author Stefan Haunsberger
#' @export
setMethod(
f = "show",
signature("MiRNANameConverter"),
definition = function(object) {
cat("An object of class: MiRNANameConverter\n");
cat("- Most recent miRBase version provided in the package:");
print(currentVersion(object));
cat("- Valid miRBase versions: ");
print(validVersions(object));
cat("- Number of species: ");
print(nOrganisms(object));
cat("- Number of database entries among all versions: ");
print(nTotalEntries(object));
}
)
##### getMirnasForMirbaseVersion ####
#' @title Retrieve two complete miRBase versions in a dataframe
#'
#' @description Return a dataframe with miRNA names from desired miRBase
#' release versions (e.g. useful for joining with other existing dataframe).
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param version Numeric vector with miRBase version (default: max version)
#' @param type Character with either \code{'mi'} or \code{'mimat'} for
#' precursor miRNA or mature miRNA names respectively (default: 'mimat')
#' @param species Character or character vector, such as \code{'hsa'} or \code{c('hsa', 'mmu')} (default: \code{'hsa'})
#' @param addLatestVersion If max-supported miRBase version is added to result set information (TRUE)
#'
#' @return A dataframe
#'
#' @examples
#' nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
#' getMirnasForMirbaseVersion(nc, version = c(18))
#'
#' @importFrom DBI dbGetQuery
#' @author Stefan J. Haunsberger
#' @rdname getMirnasForMirbaseVersion
#' @export
setGeneric(
name = "getMirnasForMirbaseVersion",
def = function(this,
version,
type = "mimat",
species = "hsa",
addLatestVersion = TRUE) {
standardGeneric("getMirnasForMirbaseVersion");
}
)
#' @describeIn getMirnasForMirbaseVersion Method for getting all miRNA names from desired miRBase version(s)
setMethod(
f = "getMirnasForMirbaseVersion",
signature("MiRNANameConverter"),
definition = function(this,
version,
type,
species,
addLatestVersion) {
args = as.list(match.call());
if (is.null(args$version)) {
version = this@.currentVersion;
}
if (addLatestVersion) {
version = c(version, this@.currentVersion);
}
if (!(type %in% c("mi", "mimat"))) {
stop(paste("type", type, "not supported (supported are 'mi' and 'mimat')"));
}
# Send SQL request
mirDf =
DBI::dbGetQuery(conn = this@.dbconn,
sprintf("SELECT accession, name, version, organism
FROM %s
WHERE version IN (%s) AND organism IN (\"%s\")
ORDER BY version ASC",
type,
paste(version, collapse = ", "), paste(species, collapse = "\", \"")));
mirDf$version = paste0("v", mirDf$version);
miRNAs.swapping = suppressMessages(assessMiRNASwappingMIMAT(this,mirDf$name));
miRNAs.not.swapping = mirDf$name[!(mirDf$name %in% miRNAs.swapping)];
if (length(miRNAs.swapping) > 0) {
if (length(miRNAs.swapping) == 1) {
message("\tFollowing miRNA will be neglected due to non unique MIMAT accession:");
} else {
message("\tFollowing miRNAs will be neglected due to non unique MIMAT accession:");
}
message(paste0(miRNAs.swapping, collapse = "; "));
}
mirDf = mirDf[!(mirDf$name %in% miRNAs.swapping),];
mirDfW = reshape2::dcast(mirDf, accession + organism ~ version, value.var = "name");
return(mirDfW);
})
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Defines functions .check
#' @title MiRNANameConverter constructor
#'
#' @description This function returns an instance of a MiRNANAmeConverter class.
#' Handling mature miRNA names from different miRBase versions
#' This package contains algorithms for dealing with mature miRNA names
#' from different miRBase release versions. The functions are provided in form
#' of methods as part of the \code{MiRNANameConverter}-class. The data of all
#' the miRBase release versions is stored in the \code{miRBaseVersions.db}
#' annotation package.
#' The \emph{MiRNAmeConverter} package contains one class that has two
#' categories of functions: getters-functions and algorithms.
#' @seealso \emph{miRBaseVersions.db} for more information about the
#' database holding all major miRBase release versions)
#'
#' @section Classes:
#' The \code{MiRNANameConverter}
# class is an S4 class that provides all the
# functions that are needed for dealing with challenges introduced over
# different miRBase releases.
#' @section Getter functions:
#' The getter functions provide access to the slots of the class.
#' @section Algorithms:
#' There are three algorithms for dealing with miRNA names from different
#' miRBase releases, the \code{\link{assessVersion}},
#' \code{\link{checkMiRNAName}} and \code{\link{translateMiRNAName}}.
#' \describe{
#' \item{\code{\link{translateMiRNAName}}}{The algorithm coded in this
#' function can translate given miRNA names to different
#' miRBase release versions.}
#' \item{\code{\link{checkMiRNAName}}}{This function is used to check if a
#' given miRNA name is listed in the current miRBase release.}
#' \item{\code{\link{assessVersion}}}{The \emph{assessVersion}}-function is
#' useful when one wants to assess the miRBase version of a given set
#' of mature miRNA names.
#' }
#'
#' @docType package
#' @name miRNAmeConverter
#'
#' @author Stefan Haunsberger \email{stefanhaunsberger@rcsi.ie}
#' @examples
#' # Translate a mature miRNA name to miRBase version 21.0
#' nc = MiRNANameConverter(); # Object instantiation
#' translateMiRNAName(nc, "hsa-miR-29a", version = 21.0)
#' @import DBI miRBaseVersions.db AnnotationDbi reshape2
NULL
# source("R/tools/printFunctionEntryInformation.R");
# source("R/tools/printFunctionExitInformation.R");
# Add package specific environment
# pkg.env <- new.env();
#' @title Instantiate from MiRNANameConverter class
#'
#' @description This function returns back an instance of a
#' \emph{MiRNANAmeConverter} object.
#'
#' @slot .dbconn Database connection
#' @slot .currentVersion Current miRBase version
#' @slot .validVersions Valid/Supported miRBase versions
#' @slot .nOrganisms Number of different organisms supported
#' @slot .nTotalEntries Total number of mature miRNA names among all provided
#' miRBase release versions in the \emph{miRBaseVersions.db} package.
#' @slot .validOrganisms Valid organisms
#' @author Stefan Haunsberger
#'
# @param this Object of class \code{MiRNANameConverter}
#' @param ... any optional arguments
MiRNANameConverter = setClass(
# Set the name for the class
Class = "MiRNANameConverter",
# Define the slots
slots = representation(
.dbconn = "SQLiteConnection",
.currentVersion = "numeric",
.validVersions = "numeric",
.nOrganisms = "integer",
.nTotalEntries = "integer",
.validOrganisms = "character"
),
# Set the default values for the slots. (optional)
prototype = list(
.dbconn = NULL,
.currentVersion = NULL,
.validVersions = NULL,
.nOrganisms = NULL,
.nTotalEntries = NULL,
.validOrganisms = NULL
)
)
##### initialization ####
# Initialization function (constructor)
setMethod(
f = "initialize",
signature("MiRNANameConverter"),
definition = function(.Object) {
# writeLines("MiRNANameConverter-constructor");
# library(miRBaseVersions.db);
args = as.list(match.call());
# Store database connection
.dbconn(.Object) = AnnotationDbi::dbconn(miRBaseVersions.db);
con = .dbconn(.Object);
# Recive all version numbers from the db
versions = (DBI::dbGetQuery(con,
"SELECT number AS version FROM version;"))$version;
validVersions(.Object) = versions;
currentVersion(.Object) = as.numeric(
AnnotationDbi::dbmeta(con,
"current_version"));
nOrganisms(.Object) =
DBI::dbGetQuery(con,
"SELECT count(DISTINCT organism) as n FROM mimat")$n;
nTotalEntries(.Object) =
DBI::dbGetQuery(con,
"SELECT count(*) as n FROM mimat")$n;
validOrganisms(.Object) =
DBI::dbGetQuery(con,
"SELECT organism FROM organism")$organism;
return(.Object);
}
)
#'
#'
.check = function(input) {
# Correct 'mir-' with 'miR-'
# output = gsub("mir-", "miR-", input, ignore.case = TRUE);
# Remove quotations (single and double)
output = gsub("\"|\'|--", "", input);
return(output);
}
##### MiRNANameConverter - constructor ####
#' @title MiRNANameConverter constructor
#'
#' @description This function returns an instance of a MiRNANAmeConverter class.
#'
#' @return an object of class 'MiRNANameConverter'
#' @examples
#' nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
#'
#' @details
#' This function initializes an object of the class MiRNANameConverter. It is a
#' wrapper for \code{new()}.
#'
#' @seealso \code{\link{new}}
#' @author Stefan Haunsberger
#' @export MiRNANameConverter
setMethod(
f = "MiRNANameConverter",
signature(),
definition = function() {
return(new('MiRNANameConverter'));
}
)
##### checkMiRNAName ####
#' @title Check miRNA names for validity
#'
#' @description This function checks for a given set of mature 'miRNAs' (names)
#' Check miRNA names for validity
#'
#' This function checks for a given set of mature 'miRNAs' (names)
#' if the names are listed in any miRBase version respectively.
#'
#' @details
#' This function takes the input miRNA names and checks each one of them for
#' validity. The check is done by taking each miRNA and searches for an existing
#' entry in the miRBase database among all versions. miRNAs that are listed in
#' any version will be comprised in the return vector respectively. If no valid
#' miRNA was detected, a \code{character(0)} will be returned.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param verbose A boolean to either show more (TRUE) or less
#' information (FALSE)
#' @return A character vector containing a set of valid miRNA names
#'
#' @examples
#' nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
#' # Test with correct inputs
#' checkMiRNAName(nc, miRNAs = c("hsa-miR-29a", "hsa-miR-642"))
#'
#' @importFrom DBI dbGetQuery
#' @author Stefan Haunsberger
#' @rdname checkMiRNAName
#' @export
setGeneric(
name = "checkMiRNAName",
def = function(this,
miRNAs,
verbose = FALSE) {
standardGeneric("checkMiRNAName");
}
)
#' @describeIn checkMiRNAName Method for checking for valid miRNA names
setMethod(
f = "checkMiRNAName",
signature("MiRNANameConverter"),
definition = function(this,
miRNAs,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'...
.\nPlease try again with a valid class.",
class(miRNAs)));
}
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
# Check which entries are acutally miRNAs listed in the miRBase repository
miRNAs.valid = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT name FROM 'vw-mimat-mirna-unique'
WHERE UPPER(name) IN (\"%s\")
ORDER BY name ASC",
paste(toupper(miRNAs.unique),
collapse = "\", \""))))$name;
n.miRNAs.valid = length(miRNAs.valid);
if (n.miRNAs.valid != length(miRNAs.unique)) {
miRNAs.invalid = miRNAs.unique[!(toupper(miRNAs.unique)
%in%
toupper(miRNAs.valid))];
if (length(miRNAs.invalid) == 1) {
message("\tThe following miRNA is not listed in the miRBase repository:");
} else {
message("\tThe following miRNAs are not listed in the miRBase repository:");
}
message(paste0(miRNAs.invalid, collapse = "; "));
}
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
# if (correct) {
# return(miRNAs.valid);
# } else {
return(miRNAs.unique[(toupper(miRNAs.unique)
%in%
toupper(miRNAs.valid))])
# }
}
)
##### assessMiRNASwappingMIMAT ####
#' @title Check if given miRNA names can be assigned to unique MIMAT
#' accessions among all versions
#'
#' @description This function checks if the names from a given set of mature
#' miRNAs have a unique MIMAT ID.
#' Check if given miRNA names can be assigned to unique MIMAT accessions among
#' all versions
#'
#' This function checks if the names from a given set of mature miRNAs
#' have a unique MIMAT ID.
#'
#' @details
#' Although the majority of miRNA names can be assigned to a unique MIMAT ID
#' (accession) some miRNAs changed MIMAT ID in different versions. This function
#' takes the input miRNA names and checks each one of them if they have a unique
#' MIMAT ID over all versions. If a miRNA changes MIMAT ID in a version it will
#' be comprised in the return vector.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param verbose A boolean to either show more (TRUE) or less information
#' (FALSE)
#' @return A character vector containing miRNA names that do not have a unique
#' MIMAT ID
#'
#' @author Stefan Haunsberger
#'
# @export
#' @rdname assessMiRNASwappingMIMAT
setGeneric(
name = "assessMiRNASwappingMIMAT",
def = function(this,
miRNAs,
verbose = FALSE) {
standardGeneric("assessMiRNASwappingMIMAT");
}
)
# @describeIn assessMiRNASwappingMIMAT Method for assessing miRNA names that
# swapped MIMAT-accession
setMethod(
f = "assessMiRNASwappingMIMAT",
signature("MiRNANameConverter"),
definition = function(this,
miRNAs,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'.\nPlease try again with a valid class.", class(miRNAs)));
}
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
# Check which entries are acutally miRNAs listed in the miRBase repository
miRNAs.swapped = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT name FROM 'vw-mimat-mirna-swapped-mimat'
WHERE UPPER(name) IN (\"%s\")
ORDER BY name ASC",
paste(toupper(miRNAs.unique), collapse = "\", \""))))$name;
n.miRNAs.swapped = length(miRNAs.swapped);
if (n.miRNAs.swapped == 1) {
message("\tFollowing miRNA does not have a unique MIMAT accession among the versions:");
message(paste0(miRNAs.swapped, collapse = "; "));
} else if (n.miRNAs.swapped > 1){
message("\tFollowing miRNAs do not have a unique MIMAT accession among the versions:");
message(paste0(miRNAs.swapped, collapse = "; "));
}
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
return(miRNAs.swapped);
}
)
##### assessVersion ####
#' @title Assess miRBase version
#'
#' @description This function detects the most likely miRBase version of a
#' given miRNA set.
#' Assess miRBase version
#'
#' This function detects the most likely miRBase version of a given miRNA set.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param verbose A boolean to either show more (TRUE) or less information (FALSE)
#' @return A data frame with two columns: version and frequency (decreasing
#' order by frequency, version)
#' + version: miRBase version
#' + frequency: the number of valid miRNAs that could be assigned
#' to the version respectively
#'
#' @examples
#' nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
#' assessVersion(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"))
#'
#' @details
#' This function takes a set of miRNA names and detects the most likely miRBase
#' version of this given set of 'miRNAs'. First all miRNAs will be checked for
#' validity (if they are actual miRNA names \code{checkMiRNAName} and the set
#' that passes the check will be further processed.
#'
#' @author Stefan Haunsberger
#' @rdname assessVersion
#' @export
setGeneric(
name = "assessVersion",
def = function(this,
miRNAs,
verbose = FALSE) {
standardGeneric("assessVersion");
}
)
#' @describeIn assessVersion Method for assessing the most likely miRBase
#' version that a given set of miRNA names is from.
setMethod(
f = "assessVersion",
signature("MiRNANameConverter"),
definition = function(this,
miRNAs,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'.\nPlease try again with a valid class.", class(miRNAs)));
}
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
# Check which entries are acutally miRNAs listed in the miRBase repository
miRNAs.valid = checkMiRNAName(this, miRNAs.unique);
n.miRNAs.valid = length(miRNAs.valid);
# Receive miRBase versions with number of assigned miRNAs
versions = DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT version, count(*) as frequency FROM mimat
WHERE UPPER(name) IN (\"%s\")
GROUP BY version
ORDER BY frequency DESC, version DESC;",
paste(toupper(miRNAs.valid), collapse = "\", \"")));
version = versions$version[1];
# Check which miRNAs could not be assigned to the identified version
n.miRNAs.not.version = 0;
if (n.miRNAs.valid != versions$frequency[1]) {
miRNAs.version = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT name FROM 'vw-mimat-%2.1f'
WHERE UPPER(name) IN (\"%s\")",
version, paste(toupper(miRNAs.valid),
collapse = "\", \""))))$name;
miRNAs.not.version = miRNAs.valid[!(toupper(miRNAs.valid)
%in%
toupper(miRNAs.version))];
n.miRNAs.not.version = length(miRNAs.not.version);
if (n.miRNAs.not.version == 1) {
message(sprintf("\tmiRNA that could not be found in identified max version %2.1f:", version));
} else {
message(sprintf("\tmiRNAs that could not be found in identified max version %2.1f:", version));
}
message(paste0(miRNAs.not.version, collapse = "; "));
}
message(sprintf("-> %i out of %i valid miRNAs assigned to max version %2.1f.", versions$frequency[1], n.miRNAs.valid, version));
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
return(versions);
}
)
##### translateMiRNAName ####
#' @title Translate miRNA name
#'
#' @description This function translates input miRNA names to different
#' miRBase versions.
#' Translate miRNA name
#'
#' This function translates input miRNA names to different miRBase versions.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param miRNAs A character vector of miRNA names
#' @param versions An integer or numerical vector containing the target versions
#' @param sequenceFormat Integer value indicating the return format for the
#' data frame containing sequence information
#' {1=only sequences, 2=miRNA name and sequence}
#' @param verbose A boolean to either show more (TRUE) or less information
#' (FALSE)
#' @return A (n x m) data frame where n is the number of valid miRNAs and m the
#' number of
#' columns (minimum 3 columns, MIMAT-ID (accession), input miRNA name, current
#' version)
#' In addition an attribute 'description' is added to the data frame where to
#' each miRNA some notes are added (for example why a certain miRNA is not
#' in the output).
#' Sequence information is attached as the attribute 'sequence'.
#'
#' @examples
#' nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
#' res = translateMiRNAName(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"),
#' versions = c(15, 16, 20, 21))
#' res
#' attributes(res)
#' @seealso \code{\link{attr}} for attributes
#'
#' @details
#' The translation and sequence retrieval are done in 5 main steps:
#' 1) Only take miRNA names that do not swap MIMAT IDs among versions
#' (\code{\link{assessMiRNASwappingMIMAT}})
#' 2) Check, if the miRNA names are valid names (\code{\link{checkMiRNAName}})
#' 3) Receive unique MIMAT IDs for each valid miRNA
#' - If there are miRNAs that have basically the same name,
#' only use miRNA names from the highest version
#' 4) Check if the found MIMAT IDs are still listed in the
#' current miRBase version
#' - If not, neglect it because then it is not considered to be a
#' miRNA anymore
#' 5) Receive names from desired versions
#'
#' @author Stefan Haunsberger
#' @rdname translateMiRNAName
#' @export
setGeneric(
name = "translateMiRNAName",
def = function(this,
miRNAs,
versions,
sequenceFormat = 1,
verbose = FALSE) {
standardGeneric("translateMiRNAName");
}
)
#' @describeIn translateMiRNAName Method for translating miRNA name(s) to
#' different miRBase versions
setMethod(
f = "translateMiRNAName",
signature(this = "MiRNANameConverter", miRNAs = "character"),
definition = function(this,
miRNAs,
versions,
sequenceFormat,
verbose) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (!is.null(args$miRNAs)) {
if (!(class(miRNAs) == "character")) {
stop(sprintf("Class of miRNAs ('%s') should be 'character'.\nPlease try again with a valid class.", class(miRNAs)));
}
# Substitute characters/clean
miRNAs = .check(miRNAs);
miRNAs.unique = unique(miRNAs);
if (length(miRNAs.unique) != length(miRNAs)) {
message(sprintf("\tInput: %i unique miRNA names",
length(miRNAs.unique)));
}
}
if (is.null(args$versions)) {
versions = this@.currentVersion;
} else {
if (!all(versions %in% this@.validVersions)) {
message(sprintf("Argument 'versions' is not valid."));
message("Valid versions are:");
message(sprintf("%2.1f", this@.validVersions));
stop("Please try again with valid 'versions' argument.");
} else {
versions = unique(versions);
}
}
# Initialize data frame with description to each miRNA
description = data.frame(input.miRNA = miRNAs.unique,
information = "OK",
stringsAsFactors = FALSE,
row.names = miRNAs.unique);
###### ### ###
# 1) Check for MIMAT swapping miRNAs
## Only use miRNAs that are not swapping MIMATs as input
miRNAs.swapping = suppressMessages(
assessMiRNASwappingMIMAT(
this,
miRNAs.unique, verbose = verbose
)
);
miRNAs.not.swapping = miRNAs.unique[!(miRNAs.unique %in% miRNAs.swapping)];
if (length(miRNAs.swapping) > 0) {
if (length(miRNAs.swapping) == 1) {
message("\tFollowing miRNA will be neglected due to non unique MIMAT accession:");
} else {
message("\tFollowing miRNAs will be neglected due to non unique MIMAT accession:");
}
message(paste0(miRNAs.swapping, collapse = "; "));
}
description[miRNAs.swapping, "information"] = "This miRNA does not have a unique MIMAT ID.";
if (length(miRNAs.not.swapping) == 0) {
message("No further miRNAs to process, return NULL.");
return(NULL);
}
###### ### ###
# 2) Check which entries are acutally miRNAs listed in the miRBase repository
## Only process miRNAs that are valid miRNA names
miRNAs.valid = suppressMessages(checkMiRNAName(this,
miRNAs.not.swapping,
verbose = verbose));
miRNAs.not.valid = miRNAs.not.swapping[!(toupper(miRNAs.not.swapping)
%in% toupper(miRNAs.valid))];
n.miRNAs.valid = length(miRNAs.valid);
n.miRNAs.dif = length(miRNAs.not.swapping) - n.miRNAs.valid;
# print(miRNAs.valid)
miRNAs.valid = suppressMessages(
checkMiRNAName(
this
,miRNAs.not.swapping
,verbose = verbose
)
);
miRNAs.not.valid = miRNAs.not.swapping[!(toupper(miRNAs.not.swapping)
%in% toupper(miRNAs.valid))];
n.miRNAs.valid = length(miRNAs.valid);
n.miRNAs.dif = length(miRNAs.not.swapping) - n.miRNAs.valid;
if (length(miRNAs.valid) == 0) {
message("No valid miRNAs found.");
return(NULL);
}
if (n.miRNAs.dif != 0) {
if (n.miRNAs.dif == 1) {
message("\tFollowing miRNA will be neglected (not listed in miRBase):");
} else {
message("\tFollowing miRNAs will be neglected (not listed in miRBase):");
}
message(paste0(miRNAs.not.valid, collapse = "; "));
}
description[miRNAs.not.valid, "information"] =
"This name is not listed in any miRBase version.";
###### ### ###
# 3) Check if there are miRNAs that have the same name -> same MIMAT
## name accession version
## e.g.: 2 hsa-let-7a* MIMAT0004481 17
## 3 hsa-let-7a-3p MIMAT0004481 21 --> would be chosen
## They are basically the same but input names are from different versions
## Receive unique MIMAT accessions for each miRNA name with the
## maximum version number
mimats.versions = DBI::dbGetQuery(
conn = .dbconn(this)
,sprintf("SELECT DISTINCT accession, name,
MAX(version) as version FROM mimat
WHERE UPPER(name) IN (\"%s\")
GROUP BY accession, name
ORDER BY accession",
paste(toupper(miRNAs.valid),
collapse = "\", \"")
)
);
if (length(miRNAs.valid) == 1) {
mimats = mimats.versions$accession;
names = mimats.versions$name;
} else {
mimats.versions.split = split(mimats.versions,
mimats.versions$accession);
mimats = character(length(unique(mimats.versions$accession)));
names = character(length(unique(mimats.versions$accession)));
for (i in 1:length(mimats.versions.split)) {
idx = 1;
if (nrow(mimats.versions.split[[i]]) > 1) {
# Take the name from the highest version
idx = which.max((mimats.versions.split[[i]])$version);
name = mimats.versions.split[[i]]$name[idx];
name.other = mimats.versions.split[[i]]$name[-idx];
writeLines(sprintf("\tmiRNA '%s' is the same as '%s'.",
name, paste(name.other, collapse = ", ")));
writeLines(sprintf("\t->%s is the most recent one and will be used. The other ones will be neglected.", name));
# Add description to miRNAs that will be neglected
description[name.other, "information"] =
sprintf("This miRNA is the same as input miRNA name '%s' from version %2.1f.",
name, (mimats.versions.split[[i]])$version[idx]);
}
mimats[i] = mimats.versions.split[[i]]$accession[idx];
names[i] = mimats.versions.split[[i]]$name[idx];
}
}
###### ### ###
# 4) Check which MIMATs are listed in the current miRBase release
## Only take miRNAs that are listed in the current version
### Receive mimats that are listed in the current version
mimats.current = (DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
this@.currentVersion, paste(toupper(mimats),
collapse = "\", \""))))$accession;
mimats.invalid = mimats[!(mimats %in% mimats.current)];
names.invalid = names[!(mimats %in% mimats.current)];
if (length(mimats.invalid) > 0) {
if (length(mimats.invalid) == 1) {
message(sprintf("\tFollowing miRNA is not listed in the current miRBase version %2.1f.",
this@.currentVersion));
} else {
message(sprintf("\tFollowing miRNAs are not listed in the current miRBase version %2.1f.",
this@.currentVersion));
}
message(paste0(names.invalid, collapse = "; "));
}
### Exclude MIMATs that are not listed in the current version
mimats.valid = mimats[mimats %in% mimats.current];
names.valid = names[mimats %in% mimats.current];
description[names.invalid, "information"] =
sprintf("This miRNA is not listed in the current miRBase version %2.1f.",
this@.currentVersion);
###### ### ###
# 5) Translate miRNA names to desired versions
## Initialize return data frame for miRNA names and sequences
### miRNA names
## Initialize return data frame
n.col = 2 + length(versions);
headers = c("mimat", "input",
paste0("v", sprintf("%2.1f",versions)));
df = as.data.frame(matrix(data = NA_character_, nrow =
length(mimats.valid), ncol = n.col));
colnames(df) = headers;
### Sequences
if (sequenceFormat == 1) {
dfSeq = as.data.frame(matrix(data = NA_character_,
nrow = length(mimats.valid),
ncol = n.col),
stringsAsFactors = FALSE);
colnames(dfSeq) = c("mimat", "input",
paste0("v", sprintf("%2.1f",versions)));
} else {
dfSeq = as.data.frame(matrix(data = NA_character_,
nrow = length(mimats.valid),
ncol = 2 + 2 * length(versions)),
stringsAsFactors = FALSE);
nam = unlist(
lapply(paste0("v", sprintf("%2.1f",versions)),
function(y1) {
lapply(c("miRNA", "Sequence"),
function(y2) {
paste(y1, y2, sep="-")
})}));
colnames(dfSeq) = c("mimat", "input", nam);
rm(nam);
}
# Convert factor columns to character columns
fac.cols = sapply(df, is.factor);
df[, fac.cols] = sapply(df[, fac.cols], as.character);
# colnames(df) = headers;
fac.cols = sapply(dfSeq, is.factor);
dfSeq[, fac.cols] = sapply(dfSeq[, fac.cols], as.character);
# colnames(dfSeq) = headers;
df$mimat = mimats.valid;
df$input = names.valid;
dfSeq$mimat = mimats.valid;
dfSeq$input = names.valid;
rownames(df) = mimats.valid;
rownames(dfSeq) = mimats.valid;
## Iterate over desired versions and
for (version in versions) {
miRNAs.version =
DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession, name FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
version, paste(toupper(df$mimat),
collapse = "\", \"")));
df[miRNAs.version$accession,
sprintf("v%2.1f",version)] = miRNAs.version$name;
# sequences
if (sequenceFormat == 1) {
# Only accession and sequence
seq.version = DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession, sequence
FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
version, paste(toupper(df$mimat),
collapse = "\", \"")));
dfSeq[seq.version$accession,
sprintf("v%2.1f",version)] = seq.version$sequence;
} else {
# Accession, miRNA name and sequence
seq.version = DBI::dbGetQuery(conn = .dbconn(this),
sprintf("SELECT accession, name, sequence
FROM 'vw-mimat-%2.1f'
WHERE accession IN (\"%s\")",
version, paste(toupper(df$mimat),
collapse = "\", \"")));
dfSeq[seq.version$accession,
sprintf("v%2.1f-Sequence",version)] = seq.version$sequence;
dfSeq[miRNAs.version$accession,
sprintf("v%2.1f-miRNA",version)] = miRNAs.version$name;
}
}
# Reorder data frames
## df by MIMAT ID
## description by input miRNA names
df = df[order(df$mimat),];
dfSeq = dfSeq[order(dfSeq$mimat),];
description = description[order(description$input.miRNA),];
# Add description as an attribute
attr(df, "description") = description;
attr(df, "sequence") = dfSeq;
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
return(df);
})
##### saveResults ####
#' @title Save miRNA translation results
#'
#' @description This function saves the data frame returned from
#' translateMiRNAName inclusive the attribute 'description'.
#' Save miRNA translation results
#'
#' This function saves the data frame returned from translateMiRNAName
#' inclusive the attribute 'description'.
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param df A \code{data.frame} with translated results
#' @param outputFilename A filename for the output file, such as 'filename.txt'
#' @param outputPath A file path (character string) to the target directory
#' @param sep Separator
#' @param quote If all data values shall be surrounded by ('"')
#' @param verbose Boolean to either show more (TRUE) or less information (FALSE)
#' @param ... Arguments that can be passed on to \code{write.table}
#'
#' @examples
#' nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
#' res = translateMiRNAName(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"),
#' versions = c(15, 16, 20, 21))
#' # Save translation results
#' saveResults(nc, res)
#'
#' @details
#' This function saves a data frame that has been returned by
#' \code{translateMiRNAName}.
#' The attribute 'description' of the data frame will be stored as well.
#'
#' @seealso \code{\link{write.table}} for additional parameter values for
#' the '...' argument, \code{\link{attr}} for how to retrieve attributes
#' @author Stefan Haunsberger
#' @rdname saveResults
#' @export
setGeneric(
name = "saveResults",
def = function(this,
df,
outputFilename,
outputPath,
sep = "\t",
quote = FALSE,
verbose = FALSE,
...) {
standardGeneric("saveResults");
}
)
#' @describeIn saveResults Method for saving translation results
setMethod(
f = "saveResults",
signature(this = "MiRNANameConverter", df = "data.frame"),
definition = function(this,
df,
outputFilename,
outputPath,
sep,
quote,
verbose,
...) {
if (verbose) {
printFunctionEntryInformation(fun = as.character((match.call())),
match_call = match.call());
}
args = as.list(match.call());
if (is.null(args$outputFilename)) {
time = format(Sys.time(), "%H%M%S");
date = format(Sys.Date(), "%d%m%Y");
outputFilename = sprintf("miRNA-name-translation-%s-%s.txt",
date, time);
}
if (is.null(args$outputPath)) {
outputPath = ".";
} else {
if (!file.exists(outputPath)) {
message(sprintf("Given outputPath '%s' does not exist.",
outputPath));
stop("Please try again with valid output path.");
}
}
# Construct 'file' (path incl. filename, such as <path>/filename.txt)
output.file = file.path(outputPath, outputFilename);
if (file.exists(output.file)) {
prefix = substr(outputFilename, 1,
sapply(gregexpr("\\.", outputFilename), tail, 1) - 1);
suffix = substr(outputFilename,
sapply(gregexpr("\\.", outputFilename), tail, 1),
nchar(outputFilename));
time = gsub(pattern = ":", replacement = "", x = (format(Sys.time(), "%X")));
date = format(Sys.Date(), "%d-%m-%Y");
outputFilename = sprintf("%s-%s-%s%s", prefix, date, time, suffix);
message(sprintf("Output file already exists -> Save file under name '%s'", outputFilename));
output.file = file.path(outputPath, outputFilename);
}
writeLines(sprintf("\tSave file to '%s'...", output.file));
utils::write.table(df, file = output.file, row.names = FALSE, quote = FALSE, sep = sep);
# description
if (!is.null(attributes(df)$description)) {
prefix = substr(outputFilename, 1,
sapply(gregexpr("\\.", outputFilename), tail, 1) - 1);
suffix = substr(outputFilename,
sapply(gregexpr("\\.", outputFilename), tail, 1),
nchar(outputFilename));
outputFilenameDesc = sprintf("%s-description%s", prefix, suffix);
output.file = file.path(outputPath, outputFilenameDesc);
writeLines(sprintf("\tSave file to '%s'...", output.file));
utils::write.table(attributes(df)$description, file = output.file,
row.names = FALSE, quote = FALSE, sep = sep);
}
if (!is.null(attributes(df)$sequence)) {
prefix = substr(outputFilename, 1,
sapply(gregexpr("\\.", outputFilename), tail, 1) - 1);
suffix = substr(outputFilename,
sapply(gregexpr("\\.", outputFilename), tail, 1),
nchar(outputFilename));
outputFilenameSeq = sprintf("%s-sequence%s", prefix, suffix);
output.file = file.path(outputPath, outputFilenameSeq);
writeLines(sprintf("\tSave file to '%s'...", output.file));
utils::write.table(attributes(df)$sequence, file = output.file,
row.names = FALSE, quote = FALSE, sep = sep);
}
if (verbose) {
printFunctionExitInformation(fun = as.character((match.call())));
}
invisible(return);
})
##### show ####
#' @title Show-method
#'
#' @description This function prints object specific information
#' Show-method
#'
#' This function prints object specific information
#'
#' @details
#' This function prints some information to the console.
#' @param object Object of class \code{MiRNANameConverter}
#' @seealso \code{\link{show}}
#'
#' @author Stefan Haunsberger
#' @export
setMethod(
f = "show",
signature("MiRNANameConverter"),
definition = function(object) {
cat("An object of class: MiRNANameConverter\n");
cat("- Most recent miRBase version provided in the package:");
print(currentVersion(object));
cat("- Valid miRBase versions: ");
print(validVersions(object));
cat("- Number of species: ");
print(nOrganisms(object));
cat("- Number of database entries among all versions: ");
print(nTotalEntries(object));
}
)
##### getMirnasForMirbaseVersion ####
#' @title Retrieve two complete miRBase versions in a dataframe
#'
#' @description Return a dataframe with miRNA names from desired miRBase
#' release versions (e.g. useful for joining with other existing dataframe).
#'
#' @param this Object of class 'MiRNANameConverter'
#' @param version Numeric vector with miRBase version (default: max version)
#' @param type Character with either \code{'mi'} or \code{'mimat'} for
#' precursor miRNA or mature miRNA names respectively (default: 'mimat')
#' @param species Character or character vector, such as \code{'hsa'} or \code{c('hsa', 'mmu')} (default: \code{'hsa'})
#' @param addLatestVersion If max-supported miRBase version is added to result set information (TRUE)
#'
#' @return A dataframe
#'
#' @examples
#' nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
#' getMirnasForMirbaseVersion(nc, version = c(18))
#'
#' @importFrom DBI dbGetQuery
#' @author Stefan J. Haunsberger
#' @rdname getMirnasForMirbaseVersion
#' @export
setGeneric(
name = "getMirnasForMirbaseVersion",
def = function(this,
version,
type = "mimat",
species = "hsa",
addLatestVersion = TRUE) {
standardGeneric("getMirnasForMirbaseVersion");
}
)
#' @describeIn getMirnasForMirbaseVersion Method for getting all miRNA names from desired miRBase version(s)
setMethod(
f = "getMirnasForMirbaseVersion",
signature("MiRNANameConverter"),
definition = function(this,
version,
type,
species,
addLatestVersion) {
args = as.list(match.call());
if (is.null(args$version)) {
version = this@.currentVersion;
}
if (addLatestVersion) {
version = c(version, this@.currentVersion);
}
if (!(type %in% c("mi", "mimat"))) {
stop(paste("type", type, "not supported (supported are 'mi' and 'mimat')"));
}
# Send SQL request
mirDf =
DBI::dbGetQuery(conn = this@.dbconn,
sprintf("SELECT accession, name, version, organism
FROM %s
WHERE version IN (%s) AND organism IN (\"%s\")
ORDER BY version ASC",
type,
paste(version, collapse = ", "), paste(species, collapse = "\", \"")));
mirDf$version = paste0("v", mirDf$version);
miRNAs.swapping = suppressMessages(assessMiRNASwappingMIMAT(this,mirDf$name));
miRNAs.not.swapping = mirDf$name[!(mirDf$name %in% miRNAs.swapping)];
if (length(miRNAs.swapping) > 0) {
if (length(miRNAs.swapping) == 1) {
message("\tFollowing miRNA will be neglected due to non unique MIMAT accession:");
} else {
message("\tFollowing miRNAs will be neglected due to non unique MIMAT accession:");
}
message(paste0(miRNAs.swapping, collapse = "; "));
}
mirDf = mirDf[!(mirDf$name %in% miRNAs.swapping),];
mirDfW = reshape2::dcast(mirDf, accession + organism ~ version, value.var = "name");
return(mirDfW);
})
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