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R/miRBaseConvert.R
In miRBaseConverter: A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
Defines functions
.getmiRNAs
goTo_miRNAFamily
checkMiRNAFamily
miRNA_MatureToPrecursor
miRNA_PrecursorToMature
getAllMiRNAs
checkMiRNAAlive
getMiRNATable
getAllSpecies
getAllVersionInfo
goTo_miRBase
checkMiRNAVersion
getMiRNAHistory
getMiRNASequence
miRNA_NameToAccession
miRNA_AccessionToName
miRNAVersionConvert
Documented in
checkMiRNAAlive
checkMiRNAFamily
checkMiRNAVersion
getAllMiRNAs
getAllSpecies
getAllVersionInfo
getMiRNAHistory
getMiRNASequence
getMiRNATable
goTo_miRBase
goTo_miRNAFamily
miRNA_AccessionToName
miRNA_MatureToPrecursor
miRNA_NameToAccession
miRNA_PrecursorToMature
miRNAVersionConvert
#' miRBase version convert for miRNA Names
#'
#' This function converts a group of any species' miRNA names (including precursor and mature miRNA) to the specified miRBase version if the miRNAs have been defined in miRBase.
#'
#' @param miRNANames A character vector representing the source miRNA names needed to be convert.
#' @param targetVersion A character value representing the target miRBase version corresponding the source miRNA names.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @param exact Logical value. If true, the result will be the most exactly matched result.
#' If FALSE, the result will include all the possible matched miRNA name. If one miRNA can match multiple names. All the matched names are
#' concatenated with "&".
#' @param verbose Logical value. If true, it will print the multiple matched miRNA Names and Accessions to the console.
#' @note Please note: Due to some miRNA names changing many times in history. Even if choose the third parameter "exact"=TRUE, it may still have some miRNAs that can't
#' match the unique name in the target version. In order to return the accurate result as possible, we also concatenate the multiple matched miRNA names with "&". This is the rare case but it happens sometimes.
#'
#' @return
#' A data frame with three columns. The number of rows equal to the input miRNA names. The three columns are defined as below:
#'\itemize{
#' \item \strong{OriginalName} : The original miRNA names (Column 1).\cr
#' \item \strong{TargetName} : The converted miRBase names (in specified version) corresponding to the original miRNA names (Column 2).\cr
#' \item \strong{Accession} : The corresponding miRBase Accessions (Column 3).
#'}
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' result1=miRNAVersionConvert(miRNANames,targetVersion="v13",exact=TRUE,verbose=TRUE)
#' result2=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE,verbose=TRUE)
#' result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=FALSE,verbose=TRUE)
#'
#' miRNANames=c( "hsa-let-7c","hsa-miR-3190-3p","hsa-let-7c","hsa-miR-34b","hsa-miR-378",
#' "hsa-miR-499a-3p","hsa-miR-499a-5p","hsa-miR-500","hsa-miR-516a-5p","hsa-miR-550","hsa-miR-589")
#' result4=miRNAVersionConvert(miRNANames, targetVersion="v22", exact=TRUE, verbose=TRUE)
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
miRNAVersionConvert <-function(miRNANames,targetVersion="v22",exact=TRUE,verbose=TRUE)
{
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
VMAP <- .getmiRNAs(targetVersion)[, c("ACC", "SYM")]
uid = unique(as.vector(miRNANames))
SYM_ID = match(uid, SYM)
df <- data.frame(uid = uid, SYM = SYM_ID, stringsAsFactors=FALSE)
df <- merge(df, ACC_SYM)[, c("uid", "ACC")]
df <- unique( merge(df, VMAP, by="ACC") )
target <- data.frame(
OriginalName = df$uid,
TargetName = SYM[df$SYM],
Accession = ACC[df$ACC],
stringsAsFactors = FALSE
)
if (exact) {
idx <- (target$OriginalName == target$TargetName) | (!target$OriginalName %in% target$TargetName)
target <- target[idx, , drop=FALSE]
}
## collapse 1:many maps
splitpaste <- function(x, f) {
result <- vapply(split(x, f), paste, character(1), collapse="&")
result[!nzchar(result)] <- NA
result
}
f <- factor(target$OriginalName, levels=uid)
target <- data.frame(
OriginalName = uid,
TargetName = splitpaste(target$TargetName, f),
Accession = splitpaste(target$Accession, f),
row.names=NULL, stringsAsFactors = FALSE
)
if(verbose)
{
multiindex=grep('&',target$TargetName)
if(length(multiindex)>0)
{
output=target[multiindex,]
colnames(output)<-c("original",paste("Version",targetVersion),"Accession")
rownames(output)<-NULL
message("********************************************\n")
message("The multiple matched miRNAs are list below: \n")
# message(" \n")
print.data.frame(output)
}
}
target=target[match(miRNANames, target$OriginalName),]
rownames(target)= NULL
target
}
#' miRBase Accession to miRNA Name in specified version
#'
#' This function converts a group of any species' miRNA Accessions (including precursor and mature miRNA) to a specified miRBase version if the Accessions have been defined in miRBase.
#'
#' @param Accessions A character vector representing the miRNA Accessions needed to be convert.
#' @param targetVersion A character value representing the target miRBase version corresponding the Accessions.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1",\cr
#' "v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A nx2 data frame. The number of rows equal to the input miRNA names. The two columns are defined as below:
#'\itemize{
#' \item \strong{Accession} : The Accession of miRNAs (Column 1).\cr
#' \item \strong{TargetName} : The converted miRBase names (in specified version) corresponding to the Accessions (Column 2).\cr
#' }
#' @examples
#' data(miRNATest)
#' Accessions=miRNATest$Accession
#' result1=miRNA_AccessionToName(Accessions,targetVersion="v13")
#' result2=miRNA_AccessionToName(Accessions,targetVersion="v22")
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
miRNA_AccessionToName<-function(Accessions,targetVersion="v22")
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
VMAP <- .getmiRNAs(targetVersion)[, c("ACC", "SYM")]
uid=unique(as.vector(Accessions))
ACC_ID=match(uid,ACC)
df=data.frame(uid = uid, ACC = ACC_ID, stringsAsFactors=FALSE)
df <- unique(merge(df, VMAP, by="ACC"))
target <- data.frame(Accession = df$uid,TargetName = SYM[df$SYM],stringsAsFactors = FALSE)
target <- target[match(Accessions, target$Accession),]
target$Accession=Accessions
rownames(target)= NULL
target
}
#' The miRBase miRNA names with specified version to Accessions
#'
#' This function converts a group of any species' miRNA name to the Accessions defined in miRBase.
#'
#' @param miRNANames A character vector representing the source miRNA names needed to be convert.
#' @param version A character value representing the version corresponding the miRNANames.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A nx2 data frame. The number of rows equal to the input miRNA names. The two columns are defined as below:
#'
#' \itemize{
#' \item \strong{miRNAName_\{Version\}} : The input miRNA names (Column 1).\cr
#' \item \strong{Accession} : The convert Accession(Column 2).\cr
#' }
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose=TRUE)
#' result1=miRNA_NameToAccession(miRNANames,version=version)
#' result2=miRNA_AccessionToName(result1[,2],targetVersion="v22")
#' result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE)
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
miRNA_NameToAccession<-function(miRNANames,version="v22")
{
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
VMAP <- .getmiRNAs(version)[, c("ACC", "SYM")]
uid=unique(as.vector(miRNANames))
SYM_ID = match(uid, SYM)
df <- data.frame(uid = uid, SYM = SYM_ID, stringsAsFactors=FALSE)
df <- unique( merge(df, VMAP, by="SYM"))
target <- data.frame(miRNANames = df$uid,Accession = ACC[df$ACC],stringsAsFactors = FALSE)
target <- target[match(miRNANames, target$miRNANames),]
target$miRNANames=miRNANames
rownames(target)= NULL
colnames(target)[1]=paste("miRNAName_",version,sep="")
target
}
#' Get the miRNA sequences
#'
#' This function returns the miRNA sequences for a list of miRNAs.
#'
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' @param targetVersion A character value representing the target miRBase version corresponding the Accessions.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A nx2 data frame. The number of row equals to input miRNAs. The two columns are defined as below:
#'
#' \itemize{
#' \item \strong{Accession} : The original miRNA (Column 1).\cr
#' \item \strong{miRNASequence_\{targetVersion\}} : The return miRNA sequence (in specified version) corresponding to the input miRNAs (Column 2).\cr
#' }
#' @examples
#' #####1, The input are miRNA Accessions
#' data(miRNATest)
#' Accessions=miRNATest$Accession
#' result1=getMiRNASequence(Accessions,targetVersion="v13")
#' result2=getMiRNASequence(Accessions,targetVersion="v22")
#'
#' #####2, The input are miRNA Names
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE)
#' Accessions=result3$Accession
#' result4=getMiRNASequence(Accessions,targetVersion="v22")
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getMiRNASequence<-function(Accessions,targetVersion="v22")
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
VMAP <- .getmiRNAs(targetVersion)[, c("ACC", "SEQ")]
uid=unique(as.vector(Accessions))
ACC_ID=match(uid,ACC)
df=data.frame(uid = uid, ACC = ACC_ID, stringsAsFactors=FALSE)
df <- unique(merge(df, VMAP, by="ACC"))
target <- data.frame(Accession = df$uid,miRNASequence = SEQ[df$SEQ],stringsAsFactors = FALSE)
target <- target[match(Accessions, target$Accession),]
target$Accession=Accessions
rownames(target)= NULL
colnames(target)[2]=paste("miRNASequence_",targetVersion,sep="")
target
}
#' Get the detailed information of a single specified miRNA in all miRBase versions.
#'
#' This function returns all available miRBase versions' information of a single specified miRNA.
#'
#' @param Accession A character representing the single Accession.
#'
#' @return
#' A data frame including all the history information (Precursor, Mature, Sequence) of the specified miRNA.
#' Each row represents a miRBase version.
#' @examples
#' #####1,The input is a miRNA Name
#' miRNAName="hsa-miR-26b-5p"
#' result1=miRNA_NameToAccession(miRNAName,version="v22")
#' Accession=result1$Accession
#' result2=getMiRNAHistory(Accession)
#'
#' #####2,The input is miRNA Accession
#' Accession="MIMAT0000765"
#' result3=getMiRNAHistory(Accession)
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getMiRNAHistory<-function(Accession)
{
Accession=as.character(Accession)
Accession=gsub(" ","",Accession)##Remove the possible space
if(length(Accession)>1)
stop("This function is only for a single miRNA query, Please query miRNAs one by one")
ACC_ID=match(Accession,ACC)
if(!is.na(ACC_ID))
{
target=data.frame(matrix(vector(),length(VER), 7,dimnames=list(c(), c("Precursor","PrecursorSequence","Mature1","Mature1Sequence","Mature2","Mature2Sequence","Status"))),stringsAsFactors=FALSE)
rownames(target)<-VER
for(i in 1:length(VER))
{
miRNAs=miRNA_data[[i]]
ind1=which(miRNAs[,c(1,5,8)] ==ACC_ID , arr.ind = TRUE)[1]
if(!is.na(ind1))
{
target[i,]=miRNAs[ind1,][c(2,4,6,7,9,10,3)]
}
}
target$Precursor=SYM[target$Precursor]
target$PrecursorSequence =SEQ[target$PrecursorSequence]
target$Mature1=SYM[target$Mature1]
target$Mature1Sequence=SEQ[target$Mature1Sequence]
target$Mature2=SYM[target$Mature2]
target$Mature2Sequence=SEQ[target$Mature2Sequence]
target$Status=STA[target$Status]
target
}
else
{
message("There is no records about this miRNA.")
NULL
}
}
#' check the miRNA Version in miRBase
#'
#' This function checks the most possible miRBase version for a list of miRNA names.
#' @importFrom stats na.omit
#' @param miRNANames A character vector representing the miRNA names.
#' @param verbose Logical value. If true, the detail version information is printed in the console for user reference.
#' @return
#' A single character value or a character vector represent the most possible miRBase version for the list of miRNA names.
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose=TRUE)
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
checkMiRNAVersion<-function(miRNANames,verbose=TRUE)
{
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
uid=unique(as.vector(miRNANames))
SYM_ID=match(uid,SYM)
SYM_ID=na.omit(SYM_ID)
#result=data.frame(matrix(vector(),length(VER), 3,dimnames=list(c(), c("Version","Proportion","Recommend") )),stringsAsFactors=FALSE)
#result$Version<-VER
result=data.frame("Version"=VER,"Proportion"=NA,"Recommend"="",stringsAsFactors=FALSE)
for(i in 1:length(VER))
{
allSYM=miRNA_data[[i]]
allSYM=c(allSYM[,2],allSYM[,6],allSYM[,9])
allSYM=na.omit(allSYM)
num =length(intersect(allSYM, SYM_ID))
result$Proportion[i]=round((num/length(uid))*100,2)
}
ind=which(result$Proportion == max(result$Proportion))
ind=rev(ind)[1]
if(verbose)
{
result[result$Proportion == max(result$Proportion), "Recommend"] <- " ***BEST Matched***"
result$Proportion=paste(result$Proportion,"%",sep="")
print.data.frame(result)
}
VER[ind]
}
#' Open the miRBase webpages of the specified miRNAs
#'
#' This function redirects the miRBase webpage of the specified miRNAs
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' We restict the number of queried miRNAs each time. The maximum number of the input miRNAs is 15.
#'
#' @examples
#' #### 1. A step-loop
#' Accession1="MI0000447"
#' goTo_miRBase(Accession1)
#'
#' #### 2. A mature miRNA
#' Accession2="MIMAT0026477"
#' goTo_miRBase(Accession2)
#'
#' #### 3. A list of miRNAs
#' Accession3=miRNATest$Accession[1:10]
#' goTo_miRBase(Accession3)
#'
#' @return
#' No values
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
goTo_miRBase<-function(Accessions)
{
Accessions=unique(Accessions)
if(length(Accessions)>15)
{
message("The number of the queried miRNAs is out of 15. Please reduce the input miRNA number")
}
else
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
alive=checkMiRNAAlive(Accessions)
for(i in alive)
{
if(grepl("MAT",i))
URL=paste0("http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=",i)
else
URL=paste0("http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=",i)
utils::browseURL(URL)
}
}
}
#' Get all miRBase version information
#'
#' This function return a reference for all miRBase versions' information including Version name,
#' Release date, miRNA number and Status.
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @return
#' The detailed version information is printed in the console for user reference.
#' @examples
#' getAllVersionInfo()
#' @export
#'
getAllVersionInfo<-function()
{
print.data.frame(VER_INFO)
}
#' Get all species of miRNAs embodied in miRBase repository
#'
#' This function return a reference for all species of miRNAs including the
#' abbreviation and full name.
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @return
#' A dataframe
#' A data frame with two columns. The two columns are defined as below:
#' \itemize{
#' \item \strong{Species} \cr
#' \item \strong{FullName} \cr
#' }
#' @examples
#' allSpecies=getAllSpecies()
#' @export
#'
getAllSpecies<-function()
{
SPE1=SPE
colnames(SPE1)[1]<-"Species"
SPE1
}
#' Get the full miRNAs information table of the specified miRBase version
#'
#' This function returns the full miRNAs information table of the specified miRBase version
#'
#' @param version A character value representing the specified miRBase version for
#' retrieval. Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @param species A character value representing the abbreviation of species. Users can apply
#' the function \strong{getAllSpecies()} to get the available abbreviation of species. If species is set
#' to \strong{"all"}, the miRNAs of all species will return.
#' @examples
#' miRNA_Tab=getMiRNATable(version="v22",species="hsa")
#' @return
#' A data frame
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getMiRNATable<-function(version="v22",species="all")
{
ver_index=match(tolower(version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
miRNA_Tab <- miRNA_data[[ver_index]]
if(species=="all")
{
miRNA_Tab=miRNA_Tab
}
else
{
spe_index=match(species,SPE$organism)
if(is.na(spe_index))
stop("It is a wrong species abbreviation, Please check it")
miRNA_Tab=miRNA_Tab[which(spe_index==miRNA_Tab$Species),]
}
miRNA_Tab$Precursor_Acc=ACC[miRNA_Tab$Precursor_Acc]
miRNA_Tab$Precursor=SYM[miRNA_Tab$Precursor]
miRNA_Tab$Status=STA[miRNA_Tab$Status]
miRNA_Tab$Precursor_Seq=SEQ[miRNA_Tab$Precursor_Seq]
miRNA_Tab$Mature1_Acc=ACC[miRNA_Tab$Mature1_Acc]
miRNA_Tab$Mature1=SYM[miRNA_Tab$Mature1]
miRNA_Tab$Mature1_Seq=SEQ[miRNA_Tab$Mature1_Seq]
miRNA_Tab$Mature2_Acc=ACC[miRNA_Tab$Mature2_Acc]
miRNA_Tab$Mature2=SYM[miRNA_Tab$Mature2]
miRNA_Tab$Mature2_Seq=SEQ[miRNA_Tab$Mature2_Seq]
miRNA_Tab[,c(1:10)]
}
#' Check the miRNA status(Alive or Dead)
#'
#' This function checks the miRNA status (Alive or Dead) in the latest miRBase version.
#'
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' @param verbose Logical value. If true, the dead miRNAs will be printed the console.
#' @examples
#' data(miRNATest)
#' ## The input is miRNA Accessions
#' Accessions=miRNATest$Accession
#' alive_Accession1=checkMiRNAAlive(Accessions)
#'
#' ##The input is miRNA names
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose = TRUE)
#' result=miRNA_NameToAccession(miRNANames,version = version)
#' Accessions=result$Accession
#' alive_Accession2=checkMiRNAAlive(Accessions)
#' @return
#' A character vector of Accessions for all alive miRNAs. The names of the return vector are the position indexes in the input Accessions.
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
checkMiRNAAlive<-function(Accessions, verbose=TRUE)
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
Accession=match(Accessions,ACC)
all_accession=.getmiRNAs()[,1]
index = is.element(Accession,all_accession)
alive=Accessions[index]
names(alive)=which(index)
if(length(which(!index)>0) && verbose)
{
dead=na.omit(unique(Accessions[!index]))
dead=data.frame("Dead.miRNAs"=dead)
message("The dead miRNAs are in below:")
print.data.frame(dead)
}
alive
}
#' Get all miRNAs in the specified miRBase version
#'
#' This function gets all miRNAs in the specified miRBase version.
#'
#' @param version A character value representing the specified miRBase version for
#' retrieval. Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1",\cr
#' "v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @param species A character value representing the abbreviation of species. Users can apply
#' the \strong{getAllSpecies()} function to get the available abbreviation of species. If species is set
#' to \strong{"all"}, the miRNAs of all species will return.
#' @param type A character value representing the miRNA type for retrieval.
#' \itemize{
#' \item \strong{"precursor"} \cr
#' \item \strong{"mature"} \cr
#' \item \strong{"all"} : precursor and mature \cr
#' }
#' @examples
#' miRNAs=getAllMiRNAs(version="v22", type="all", species="hsa")
#' @return
#' A data frame with three columns. The three columns are defined as below:
#' \itemize{
#' \item \strong{Accession} \cr
#' \item \strong{Name} \cr
#' \item \strong{Sequence} \cr
#' }
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getAllMiRNAs<-function(version="v22",type="all",species="all")
{
ver_index=match(tolower(version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
MiRNAs <- miRNA_data[[ver_index]]
if(species=="all")
{
MiRNAs=MiRNAs
}
else
{
spe_index=match(species,SPE$organism)
if(is.na(spe_index))
stop("It is a wrong species abbreviation, Please check it")
MiRNAs=MiRNAs[which(spe_index==MiRNAs$Species),]
}
if(type=="all")
{
Precursor=MiRNAs[,c(1,2,4)]
Mature1=MiRNAs[,c(5,6,7)]
Mature2=MiRNAs[,c(8,9,10)]
colnames(Precursor)=c("Accession","Name","Sequence")
colnames(Mature1)=c("Accession","Name","Sequence")
colnames(Mature2)=c("Accession","Name","Sequence")
MiRNAs=rbind.data.frame(Precursor,Mature1,Mature2)
}
else if(type=="precursor")
{
MiRNAs=MiRNAs[,c(1,2,4)]
colnames(MiRNAs)=c("Accession","Name","Sequence")
}
else if(type=="mature")
{
Mature1=MiRNAs[,c(5,6,7)]
Mature2=MiRNAs[,c(8,9,10)]
colnames(Mature1)=c("Accession","Name","Sequence")
colnames(Mature2)=c("Accession","Name","Sequence")
MiRNAs=rbind(Mature1,Mature2)
}
else
stop("It is a wrong miRNA type parameter, Please check it")
#MiRNAs=na.omit(MiRNAs)
ind <-which(apply(MiRNAs, 1, function(x) all(is.na(x))))
MiRNAs=MiRNAs[-ind,]
MiRNAs=unique(MiRNAs)
MiRNAs$Accession=ACC[MiRNAs$Accession]
MiRNAs$Name=SYM[MiRNAs$Name]
MiRNAs$Sequence=SEQ[MiRNAs$Sequence]
MiRNAs=MiRNAs[order(MiRNAs$Name),]
rownames(MiRNAs)=NULL
MiRNAs
}
#' Convert the precursors to the corresponding mature miRNAs
#'
#' This function converts the precursors to the corresponding mature miRNAs in the specified miRBase version.
#' @param miRNANames A character vector representing the miRNA names.
#' @param version The default is \strong{NULL} representing the most possible latest version of the input miRNA Names will be checked automatically.
#' Otherwise, a character value representing the version corresponding the input miRNA Names.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A data frame(nx3). The number of rows equal to the input miRNA names. The three columns are defined as below:
#' \itemize{
#' \item \strong{OriginalName} : The input miRNA Names.\cr
#' \item \strong{Mature1} : The corresponding mature miRNAs (always "-5p") .\cr
#' \item \strong{Mature2} : The corresponding mature miRNAs (always "-3p") .\cr
#' }
#'
#' @note
#' If the input miRNA Names mingle mature miRNA names, the mature miRNA names will match to themselves in the output.
#'
#' @examples
#' miRNANames=c("pma-mir-100a","sko-mir-92a","hsa-mir-6131","mtr-MIR2655i",
#' "mmu-mir-153","mtr-MIR2592am","mml-mir-1239","xtr-mir-128-2","oan-mir-100",
#' "mmu-mir-378b","hsa-miR-508-5p","mmu-miR-434-3p")
#' result=miRNA_PrecursorToMature(miRNANames)
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
miRNA_PrecursorToMature<-function(miRNANames,version=NULL)
{
if(is.null(version))
{
c_version=checkMiRNAVersion(miRNANames,verbose = FALSE)
cat(paste0("The input miRNA version information: miRBase ",c_version))
}
else
c_version=version
ver_index=match(tolower(c_version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
VMAP <-miRNA_data[[ver_index]][,c(2,6,9)]
VMAP[,1]=SYM[VMAP[,1]]
VMAP[,2]=SYM[VMAP[,2]]
VMAP[,3]=SYM[VMAP[,3]]
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
uid = unique(as.vector(miRNANames))
uid=na.omit(uid)
ind=apply(VMAP,2,function(x){match(uid,x)})
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),2]
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),3]
target <- data.frame(
OriginalName = uid,
Mature1 = VMAP[ind[,1],2],
Mature2 = VMAP[ind[,1],3],
row.names=NULL, stringsAsFactors = FALSE)
target=target[match(miRNANames, target$OriginalName),]
rownames(target)=NULL
target
}
#' Convert the mature miRNAs to the corresponding precursors
#'
#' This function converts the mature miRNAs to the corresponding precursors in the specified miRBase version.
#' @param miRNANames A character vector representing the miRNA names.
#' @param version The default is \strong{NULL} representing the most possible latest version of the input miRNA Names will be checked automatically.
#' Otherwise, a character value representing the version corresponding the input miRNA Names.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A data frame(nx2). The number of rows equal to the input miRNA Names. The two columns are defined as below:
#' \itemize{
#' \item \strong{OriginalName} : The input miRNA Names.\cr
#' \item \strong{Precursor} : The corresponding precursors of the mature miRNAs.\cr
#' }
#'
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' result=miRNA_MatureToPrecursor(miRNANames)
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
miRNA_MatureToPrecursor<-function(miRNANames,version=NULL)
{
if(is.null(version))
{
c_version=rev(checkMiRNAVersion(miRNANames,verbose = FALSE))[1]
cat(paste0("The input miRNA version information: miRBase ",c_version))
}
else
c_version=version
ver_index=match(tolower(c_version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
VMAP <-miRNA_data[[ver_index]][,c(2,6,9)]
VMAP[,1]=SYM[VMAP[,1]]
VMAP[,2]=SYM[VMAP[,2]]
VMAP[,3]=SYM[VMAP[,3]]
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
uid = unique(as.vector(miRNANames))
uid=na.omit(uid)
ind=apply(VMAP,2,function(x){match(uid,x)})
ind[which(is.na(ind[,2])),2]=ind[which(is.na(ind[,2])),3]
ind[which(is.na(ind[,2])),2]=ind[which(is.na(ind[,2])),1]
target <- data.frame(
OriginalName = uid,
Precursor = VMAP[ind[,2],1],
row.names=NULL, stringsAsFactors = FALSE)
target=target[match(miRNANames, target$OriginalName),]
rownames(target)=NULL
target
}
#' Check the miRNA family
#'
#' This function checks the miRNA family for a list of miRNA Names.
#'
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' @examples
#' data(miRNATest)
#' ## The input is miRNA Accessions
#' Accessions=miRNATest$Accession
#' Family_Info1=checkMiRNAFamily(Accessions)
#'
#' ##The input is miRNA names
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose = TRUE)
#' result=miRNA_NameToAccession(miRNANames,version=version)
#' Accessions=result$Accession
#' Family_Info2=checkMiRNAFamily(Accessions)
#'
#' @return
#' A data frame with four columns. The number of rows equal to the input Accessions. The four columns are defined as below:
#' \itemize{
#' \item \strong{Accession} : The input miRNA accessions.\cr
#' \item \strong{miRNAName_v21} : The miRNA names (version 21) corresponding to the Accession.\cr
#' \item \strong{FamilyAccession} : The accession of the family .\cr
#' \item \strong{Family} : The family name.\cr
#' }
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
checkMiRNAFamily<-function(Accessions)
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
uid=unique(as.vector(Accessions))
uid=na.omit(uid)
miRNANames=miRNA_AccessionToName(uid)
ACC_ID=match(uid,ACC)
#v21
VMAP <-miRNA_data[[21]][,c(1,5,8,12)]
ind=apply(VMAP,2,function(x){match(ACC_ID,x)})
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),2]
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),3]
xx=FAM[VMAP$FAM[ind[,1]],]
target=data.frame(miRNANames,xx,stringsAsFactors=FALSE)
target=target[match(Accessions,target$Accession),]
rownames(target)=NULL
colnames(target)=c("Accession","miRNAName_v21","FamilyAccession","Family")
target
}
#' Open the miRNA family webpages of the specified miRNAs
#'
#' This function redirects the miRBase miRNA family webpages of the specified miRNA families
#'
#' @param FamilyAccessions A character vector representing the miRNA family Accessions in miRBase.
#' We restict the queried number of miRNA family each time. The maximum number of the input miRNA families is 15.
#' @param verbose Logical value. If true, the invalid miRNA Family will be printed the console.
#'
#' @examples
#' data(miRNATest)
#' Accessions=miRNATest$Accession
#' Family_Info=checkMiRNAFamily(Accessions)
#' FamilyAccessions=Family_Info$FamilyAccession[1:15]
#' goTo_miRNAFamily(FamilyAccessions)
#' @return
#' No values
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
goTo_miRNAFamily<-function(FamilyAccessions, verbose = TRUE)
{
FamilyAccessions=unique(FamilyAccessions)
FamilyAccessions=na.omit(FamilyAccessions)
if(length(FamilyAccessions)>15)
{
message("The number of the queried miRNA familys is out of 15. Please reduce the input miRNA family number")
}
else
{
ind=match(FamilyAccessions,FAM$FAM_ACC)
ind1=which(is.na(ind))
ind2=which(!is.na(ind))
dead=FamilyAccessions[ind1]
alive=FamilyAccessions[ind2]
if(length(dead)>0 && verbose)
{
dead=data.frame("Invalid.miRNAFamily"=dead)
message("The invalid Family Accessions are in below: ")
print.data.frame(dead)
}
for(i in alive)
{
URL=paste0("http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=",i)
utils::browseURL(URL)
}
}
}
###internal function
.getmiRNAs<-function(version="v22")
{
ver_index=match(tolower(version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
#MiRNAs <- as.matrix(miRNA_data[[ver_index]])
MiRNAs <- miRNA_data[[ver_index]]
Precursor=MiRNAs[,c(1,2,4)]
Mature1=MiRNAs[,c(5,6,7)]
Mature2=MiRNAs[,c(8,9,10)]
colnames(Precursor)=c("ACC","SYM","SEQ")
colnames(Mature1)=c("ACC","SYM","SEQ")
colnames(Mature2)=c("ACC","SYM","SEQ")
MiRNAs=rbind.data.frame(Precursor,Mature1,Mature2)
#MiRNAs=na.omit(MiRNAs)
##check the rows with all NA
ind <- which(apply(MiRNAs, 1, function(x) all(is.na(x))))
MiRNAs=MiRNAs[-ind,]
MiRNAs=unique(MiRNAs)
#MiRNAs=as.data.frame(MiRNAs,stringsAsFactors=FALSE)
MiRNAs
}
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Defines functions .getmiRNAs goTo_miRNAFamily checkMiRNAFamily miRNA_MatureToPrecursor miRNA_PrecursorToMature getAllMiRNAs checkMiRNAAlive getMiRNATable getAllSpecies getAllVersionInfo goTo_miRBase checkMiRNAVersion getMiRNAHistory getMiRNASequence miRNA_NameToAccession miRNA_AccessionToName miRNAVersionConvert
Documented in checkMiRNAAlive checkMiRNAFamily checkMiRNAVersion getAllMiRNAs getAllSpecies getAllVersionInfo getMiRNAHistory getMiRNASequence getMiRNATable goTo_miRBase goTo_miRNAFamily miRNA_AccessionToName miRNA_MatureToPrecursor miRNA_NameToAccession miRNA_PrecursorToMature miRNAVersionConvert
#' miRBase version convert for miRNA Names
#'
#' This function converts a group of any species' miRNA names (including precursor and mature miRNA) to the specified miRBase version if the miRNAs have been defined in miRBase.
#'
#' @param miRNANames A character vector representing the source miRNA names needed to be convert.
#' @param targetVersion A character value representing the target miRBase version corresponding the source miRNA names.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @param exact Logical value. If true, the result will be the most exactly matched result.
#' If FALSE, the result will include all the possible matched miRNA name. If one miRNA can match multiple names. All the matched names are
#' concatenated with "&".
#' @param verbose Logical value. If true, it will print the multiple matched miRNA Names and Accessions to the console.
#' @note Please note: Due to some miRNA names changing many times in history. Even if choose the third parameter "exact"=TRUE, it may still have some miRNAs that can't
#' match the unique name in the target version. In order to return the accurate result as possible, we also concatenate the multiple matched miRNA names with "&". This is the rare case but it happens sometimes.
#'
#' @return
#' A data frame with three columns. The number of rows equal to the input miRNA names. The three columns are defined as below:
#'\itemize{
#' \item \strong{OriginalName} : The original miRNA names (Column 1).\cr
#' \item \strong{TargetName} : The converted miRBase names (in specified version) corresponding to the original miRNA names (Column 2).\cr
#' \item \strong{Accession} : The corresponding miRBase Accessions (Column 3).
#'}
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' result1=miRNAVersionConvert(miRNANames,targetVersion="v13",exact=TRUE,verbose=TRUE)
#' result2=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE,verbose=TRUE)
#' result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=FALSE,verbose=TRUE)
#'
#' miRNANames=c( "hsa-let-7c","hsa-miR-3190-3p","hsa-let-7c","hsa-miR-34b","hsa-miR-378",
#' "hsa-miR-499a-3p","hsa-miR-499a-5p","hsa-miR-500","hsa-miR-516a-5p","hsa-miR-550","hsa-miR-589")
#' result4=miRNAVersionConvert(miRNANames, targetVersion="v22", exact=TRUE, verbose=TRUE)
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
miRNAVersionConvert <-function(miRNANames,targetVersion="v22",exact=TRUE,verbose=TRUE)
{
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
VMAP <- .getmiRNAs(targetVersion)[, c("ACC", "SYM")]
uid = unique(as.vector(miRNANames))
SYM_ID = match(uid, SYM)
df <- data.frame(uid = uid, SYM = SYM_ID, stringsAsFactors=FALSE)
df <- merge(df, ACC_SYM)[, c("uid", "ACC")]
df <- unique( merge(df, VMAP, by="ACC") )
target <- data.frame(
OriginalName = df$uid,
TargetName = SYM[df$SYM],
Accession = ACC[df$ACC],
stringsAsFactors = FALSE
)
if (exact) {
idx <- (target$OriginalName == target$TargetName) | (!target$OriginalName %in% target$TargetName)
target <- target[idx, , drop=FALSE]
}
## collapse 1:many maps
splitpaste <- function(x, f) {
result <- vapply(split(x, f), paste, character(1), collapse="&")
result[!nzchar(result)] <- NA
result
}
f <- factor(target$OriginalName, levels=uid)
target <- data.frame(
OriginalName = uid,
TargetName = splitpaste(target$TargetName, f),
Accession = splitpaste(target$Accession, f),
row.names=NULL, stringsAsFactors = FALSE
)
if(verbose)
{
multiindex=grep('&',target$TargetName)
if(length(multiindex)>0)
{
output=target[multiindex,]
colnames(output)<-c("original",paste("Version",targetVersion),"Accession")
rownames(output)<-NULL
message("********************************************\n")
message("The multiple matched miRNAs are list below: \n")
# message(" \n")
print.data.frame(output)
}
}
target=target[match(miRNANames, target$OriginalName),]
rownames(target)= NULL
target
}
#' miRBase Accession to miRNA Name in specified version
#'
#' This function converts a group of any species' miRNA Accessions (including precursor and mature miRNA) to a specified miRBase version if the Accessions have been defined in miRBase.
#'
#' @param Accessions A character vector representing the miRNA Accessions needed to be convert.
#' @param targetVersion A character value representing the target miRBase version corresponding the Accessions.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1",\cr
#' "v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A nx2 data frame. The number of rows equal to the input miRNA names. The two columns are defined as below:
#'\itemize{
#' \item \strong{Accession} : The Accession of miRNAs (Column 1).\cr
#' \item \strong{TargetName} : The converted miRBase names (in specified version) corresponding to the Accessions (Column 2).\cr
#' }
#' @examples
#' data(miRNATest)
#' Accessions=miRNATest$Accession
#' result1=miRNA_AccessionToName(Accessions,targetVersion="v13")
#' result2=miRNA_AccessionToName(Accessions,targetVersion="v22")
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
miRNA_AccessionToName<-function(Accessions,targetVersion="v22")
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
VMAP <- .getmiRNAs(targetVersion)[, c("ACC", "SYM")]
uid=unique(as.vector(Accessions))
ACC_ID=match(uid,ACC)
df=data.frame(uid = uid, ACC = ACC_ID, stringsAsFactors=FALSE)
df <- unique(merge(df, VMAP, by="ACC"))
target <- data.frame(Accession = df$uid,TargetName = SYM[df$SYM],stringsAsFactors = FALSE)
target <- target[match(Accessions, target$Accession),]
target$Accession=Accessions
rownames(target)= NULL
target
}
#' The miRBase miRNA names with specified version to Accessions
#'
#' This function converts a group of any species' miRNA name to the Accessions defined in miRBase.
#'
#' @param miRNANames A character vector representing the source miRNA names needed to be convert.
#' @param version A character value representing the version corresponding the miRNANames.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A nx2 data frame. The number of rows equal to the input miRNA names. The two columns are defined as below:
#'
#' \itemize{
#' \item \strong{miRNAName_\{Version\}} : The input miRNA names (Column 1).\cr
#' \item \strong{Accession} : The convert Accession(Column 2).\cr
#' }
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose=TRUE)
#' result1=miRNA_NameToAccession(miRNANames,version=version)
#' result2=miRNA_AccessionToName(result1[,2],targetVersion="v22")
#' result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE)
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
miRNA_NameToAccession<-function(miRNANames,version="v22")
{
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
VMAP <- .getmiRNAs(version)[, c("ACC", "SYM")]
uid=unique(as.vector(miRNANames))
SYM_ID = match(uid, SYM)
df <- data.frame(uid = uid, SYM = SYM_ID, stringsAsFactors=FALSE)
df <- unique( merge(df, VMAP, by="SYM"))
target <- data.frame(miRNANames = df$uid,Accession = ACC[df$ACC],stringsAsFactors = FALSE)
target <- target[match(miRNANames, target$miRNANames),]
target$miRNANames=miRNANames
rownames(target)= NULL
colnames(target)[1]=paste("miRNAName_",version,sep="")
target
}
#' Get the miRNA sequences
#'
#' This function returns the miRNA sequences for a list of miRNAs.
#'
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' @param targetVersion A character value representing the target miRBase version corresponding the Accessions.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A nx2 data frame. The number of row equals to input miRNAs. The two columns are defined as below:
#'
#' \itemize{
#' \item \strong{Accession} : The original miRNA (Column 1).\cr
#' \item \strong{miRNASequence_\{targetVersion\}} : The return miRNA sequence (in specified version) corresponding to the input miRNAs (Column 2).\cr
#' }
#' @examples
#' #####1, The input are miRNA Accessions
#' data(miRNATest)
#' Accessions=miRNATest$Accession
#' result1=getMiRNASequence(Accessions,targetVersion="v13")
#' result2=getMiRNASequence(Accessions,targetVersion="v22")
#'
#' #####2, The input are miRNA Names
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE)
#' Accessions=result3$Accession
#' result4=getMiRNASequence(Accessions,targetVersion="v22")
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getMiRNASequence<-function(Accessions,targetVersion="v22")
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
VMAP <- .getmiRNAs(targetVersion)[, c("ACC", "SEQ")]
uid=unique(as.vector(Accessions))
ACC_ID=match(uid,ACC)
df=data.frame(uid = uid, ACC = ACC_ID, stringsAsFactors=FALSE)
df <- unique(merge(df, VMAP, by="ACC"))
target <- data.frame(Accession = df$uid,miRNASequence = SEQ[df$SEQ],stringsAsFactors = FALSE)
target <- target[match(Accessions, target$Accession),]
target$Accession=Accessions
rownames(target)= NULL
colnames(target)[2]=paste("miRNASequence_",targetVersion,sep="")
target
}
#' Get the detailed information of a single specified miRNA in all miRBase versions.
#'
#' This function returns all available miRBase versions' information of a single specified miRNA.
#'
#' @param Accession A character representing the single Accession.
#'
#' @return
#' A data frame including all the history information (Precursor, Mature, Sequence) of the specified miRNA.
#' Each row represents a miRBase version.
#' @examples
#' #####1,The input is a miRNA Name
#' miRNAName="hsa-miR-26b-5p"
#' result1=miRNA_NameToAccession(miRNAName,version="v22")
#' Accession=result1$Accession
#' result2=getMiRNAHistory(Accession)
#'
#' #####2,The input is miRNA Accession
#' Accession="MIMAT0000765"
#' result3=getMiRNAHistory(Accession)
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getMiRNAHistory<-function(Accession)
{
Accession=as.character(Accession)
Accession=gsub(" ","",Accession)##Remove the possible space
if(length(Accession)>1)
stop("This function is only for a single miRNA query, Please query miRNAs one by one")
ACC_ID=match(Accession,ACC)
if(!is.na(ACC_ID))
{
target=data.frame(matrix(vector(),length(VER), 7,dimnames=list(c(), c("Precursor","PrecursorSequence","Mature1","Mature1Sequence","Mature2","Mature2Sequence","Status"))),stringsAsFactors=FALSE)
rownames(target)<-VER
for(i in 1:length(VER))
{
miRNAs=miRNA_data[[i]]
ind1=which(miRNAs[,c(1,5,8)] ==ACC_ID , arr.ind = TRUE)[1]
if(!is.na(ind1))
{
target[i,]=miRNAs[ind1,][c(2,4,6,7,9,10,3)]
}
}
target$Precursor=SYM[target$Precursor]
target$PrecursorSequence =SEQ[target$PrecursorSequence]
target$Mature1=SYM[target$Mature1]
target$Mature1Sequence=SEQ[target$Mature1Sequence]
target$Mature2=SYM[target$Mature2]
target$Mature2Sequence=SEQ[target$Mature2Sequence]
target$Status=STA[target$Status]
target
}
else
{
message("There is no records about this miRNA.")
NULL
}
}
#' check the miRNA Version in miRBase
#'
#' This function checks the most possible miRBase version for a list of miRNA names.
#' @importFrom stats na.omit
#' @param miRNANames A character vector representing the miRNA names.
#' @param verbose Logical value. If true, the detail version information is printed in the console for user reference.
#' @return
#' A single character value or a character vector represent the most possible miRBase version for the list of miRNA names.
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose=TRUE)
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
checkMiRNAVersion<-function(miRNANames,verbose=TRUE)
{
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
uid=unique(as.vector(miRNANames))
SYM_ID=match(uid,SYM)
SYM_ID=na.omit(SYM_ID)
#result=data.frame(matrix(vector(),length(VER), 3,dimnames=list(c(), c("Version","Proportion","Recommend") )),stringsAsFactors=FALSE)
#result$Version<-VER
result=data.frame("Version"=VER,"Proportion"=NA,"Recommend"="",stringsAsFactors=FALSE)
for(i in 1:length(VER))
{
allSYM=miRNA_data[[i]]
allSYM=c(allSYM[,2],allSYM[,6],allSYM[,9])
allSYM=na.omit(allSYM)
num =length(intersect(allSYM, SYM_ID))
result$Proportion[i]=round((num/length(uid))*100,2)
}
ind=which(result$Proportion == max(result$Proportion))
ind=rev(ind)[1]
if(verbose)
{
result[result$Proportion == max(result$Proportion), "Recommend"] <- " ***BEST Matched***"
result$Proportion=paste(result$Proportion,"%",sep="")
print.data.frame(result)
}
VER[ind]
}
#' Open the miRBase webpages of the specified miRNAs
#'
#' This function redirects the miRBase webpage of the specified miRNAs
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' We restict the number of queried miRNAs each time. The maximum number of the input miRNAs is 15.
#'
#' @examples
#' #### 1. A step-loop
#' Accession1="MI0000447"
#' goTo_miRBase(Accession1)
#'
#' #### 2. A mature miRNA
#' Accession2="MIMAT0026477"
#' goTo_miRBase(Accession2)
#'
#' #### 3. A list of miRNAs
#' Accession3=miRNATest$Accession[1:10]
#' goTo_miRBase(Accession3)
#'
#' @return
#' No values
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
goTo_miRBase<-function(Accessions)
{
Accessions=unique(Accessions)
if(length(Accessions)>15)
{
message("The number of the queried miRNAs is out of 15. Please reduce the input miRNA number")
}
else
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
alive=checkMiRNAAlive(Accessions)
for(i in alive)
{
if(grepl("MAT",i))
URL=paste0("http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=",i)
else
URL=paste0("http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=",i)
utils::browseURL(URL)
}
}
}
#' Get all miRBase version information
#'
#' This function return a reference for all miRBase versions' information including Version name,
#' Release date, miRNA number and Status.
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @return
#' The detailed version information is printed in the console for user reference.
#' @examples
#' getAllVersionInfo()
#' @export
#'
getAllVersionInfo<-function()
{
print.data.frame(VER_INFO)
}
#' Get all species of miRNAs embodied in miRBase repository
#'
#' This function return a reference for all species of miRNAs including the
#' abbreviation and full name.
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @return
#' A dataframe
#' A data frame with two columns. The two columns are defined as below:
#' \itemize{
#' \item \strong{Species} \cr
#' \item \strong{FullName} \cr
#' }
#' @examples
#' allSpecies=getAllSpecies()
#' @export
#'
getAllSpecies<-function()
{
SPE1=SPE
colnames(SPE1)[1]<-"Species"
SPE1
}
#' Get the full miRNAs information table of the specified miRBase version
#'
#' This function returns the full miRNAs information table of the specified miRBase version
#'
#' @param version A character value representing the specified miRBase version for
#' retrieval. Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @param species A character value representing the abbreviation of species. Users can apply
#' the function \strong{getAllSpecies()} to get the available abbreviation of species. If species is set
#' to \strong{"all"}, the miRNAs of all species will return.
#' @examples
#' miRNA_Tab=getMiRNATable(version="v22",species="hsa")
#' @return
#' A data frame
#'
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getMiRNATable<-function(version="v22",species="all")
{
ver_index=match(tolower(version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
miRNA_Tab <- miRNA_data[[ver_index]]
if(species=="all")
{
miRNA_Tab=miRNA_Tab
}
else
{
spe_index=match(species,SPE$organism)
if(is.na(spe_index))
stop("It is a wrong species abbreviation, Please check it")
miRNA_Tab=miRNA_Tab[which(spe_index==miRNA_Tab$Species),]
}
miRNA_Tab$Precursor_Acc=ACC[miRNA_Tab$Precursor_Acc]
miRNA_Tab$Precursor=SYM[miRNA_Tab$Precursor]
miRNA_Tab$Status=STA[miRNA_Tab$Status]
miRNA_Tab$Precursor_Seq=SEQ[miRNA_Tab$Precursor_Seq]
miRNA_Tab$Mature1_Acc=ACC[miRNA_Tab$Mature1_Acc]
miRNA_Tab$Mature1=SYM[miRNA_Tab$Mature1]
miRNA_Tab$Mature1_Seq=SEQ[miRNA_Tab$Mature1_Seq]
miRNA_Tab$Mature2_Acc=ACC[miRNA_Tab$Mature2_Acc]
miRNA_Tab$Mature2=SYM[miRNA_Tab$Mature2]
miRNA_Tab$Mature2_Seq=SEQ[miRNA_Tab$Mature2_Seq]
miRNA_Tab[,c(1:10)]
}
#' Check the miRNA status(Alive or Dead)
#'
#' This function checks the miRNA status (Alive or Dead) in the latest miRBase version.
#'
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' @param verbose Logical value. If true, the dead miRNAs will be printed the console.
#' @examples
#' data(miRNATest)
#' ## The input is miRNA Accessions
#' Accessions=miRNATest$Accession
#' alive_Accession1=checkMiRNAAlive(Accessions)
#'
#' ##The input is miRNA names
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose = TRUE)
#' result=miRNA_NameToAccession(miRNANames,version = version)
#' Accessions=result$Accession
#' alive_Accession2=checkMiRNAAlive(Accessions)
#' @return
#' A character vector of Accessions for all alive miRNAs. The names of the return vector are the position indexes in the input Accessions.
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
checkMiRNAAlive<-function(Accessions, verbose=TRUE)
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
Accession=match(Accessions,ACC)
all_accession=.getmiRNAs()[,1]
index = is.element(Accession,all_accession)
alive=Accessions[index]
names(alive)=which(index)
if(length(which(!index)>0) && verbose)
{
dead=na.omit(unique(Accessions[!index]))
dead=data.frame("Dead.miRNAs"=dead)
message("The dead miRNAs are in below:")
print.data.frame(dead)
}
alive
}
#' Get all miRNAs in the specified miRBase version
#'
#' This function gets all miRNAs in the specified miRBase version.
#'
#' @param version A character value representing the specified miRBase version for
#' retrieval. Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1",\cr
#' "v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @param species A character value representing the abbreviation of species. Users can apply
#' the \strong{getAllSpecies()} function to get the available abbreviation of species. If species is set
#' to \strong{"all"}, the miRNAs of all species will return.
#' @param type A character value representing the miRNA type for retrieval.
#' \itemize{
#' \item \strong{"precursor"} \cr
#' \item \strong{"mature"} \cr
#' \item \strong{"all"} : precursor and mature \cr
#' }
#' @examples
#' miRNAs=getAllMiRNAs(version="v22", type="all", species="hsa")
#' @return
#' A data frame with three columns. The three columns are defined as below:
#' \itemize{
#' \item \strong{Accession} \cr
#' \item \strong{Name} \cr
#' \item \strong{Sequence} \cr
#' }
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
getAllMiRNAs<-function(version="v22",type="all",species="all")
{
ver_index=match(tolower(version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
MiRNAs <- miRNA_data[[ver_index]]
if(species=="all")
{
MiRNAs=MiRNAs
}
else
{
spe_index=match(species,SPE$organism)
if(is.na(spe_index))
stop("It is a wrong species abbreviation, Please check it")
MiRNAs=MiRNAs[which(spe_index==MiRNAs$Species),]
}
if(type=="all")
{
Precursor=MiRNAs[,c(1,2,4)]
Mature1=MiRNAs[,c(5,6,7)]
Mature2=MiRNAs[,c(8,9,10)]
colnames(Precursor)=c("Accession","Name","Sequence")
colnames(Mature1)=c("Accession","Name","Sequence")
colnames(Mature2)=c("Accession","Name","Sequence")
MiRNAs=rbind.data.frame(Precursor,Mature1,Mature2)
}
else if(type=="precursor")
{
MiRNAs=MiRNAs[,c(1,2,4)]
colnames(MiRNAs)=c("Accession","Name","Sequence")
}
else if(type=="mature")
{
Mature1=MiRNAs[,c(5,6,7)]
Mature2=MiRNAs[,c(8,9,10)]
colnames(Mature1)=c("Accession","Name","Sequence")
colnames(Mature2)=c("Accession","Name","Sequence")
MiRNAs=rbind(Mature1,Mature2)
}
else
stop("It is a wrong miRNA type parameter, Please check it")
#MiRNAs=na.omit(MiRNAs)
ind <-which(apply(MiRNAs, 1, function(x) all(is.na(x))))
MiRNAs=MiRNAs[-ind,]
MiRNAs=unique(MiRNAs)
MiRNAs$Accession=ACC[MiRNAs$Accession]
MiRNAs$Name=SYM[MiRNAs$Name]
MiRNAs$Sequence=SEQ[MiRNAs$Sequence]
MiRNAs=MiRNAs[order(MiRNAs$Name),]
rownames(MiRNAs)=NULL
MiRNAs
}
#' Convert the precursors to the corresponding mature miRNAs
#'
#' This function converts the precursors to the corresponding mature miRNAs in the specified miRBase version.
#' @param miRNANames A character vector representing the miRNA names.
#' @param version The default is \strong{NULL} representing the most possible latest version of the input miRNA Names will be checked automatically.
#' Otherwise, a character value representing the version corresponding the input miRNA Names.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A data frame(nx3). The number of rows equal to the input miRNA names. The three columns are defined as below:
#' \itemize{
#' \item \strong{OriginalName} : The input miRNA Names.\cr
#' \item \strong{Mature1} : The corresponding mature miRNAs (always "-5p") .\cr
#' \item \strong{Mature2} : The corresponding mature miRNAs (always "-3p") .\cr
#' }
#'
#' @note
#' If the input miRNA Names mingle mature miRNA names, the mature miRNA names will match to themselves in the output.
#'
#' @examples
#' miRNANames=c("pma-mir-100a","sko-mir-92a","hsa-mir-6131","mtr-MIR2655i",
#' "mmu-mir-153","mtr-MIR2592am","mml-mir-1239","xtr-mir-128-2","oan-mir-100",
#' "mmu-mir-378b","hsa-miR-508-5p","mmu-miR-434-3p")
#' result=miRNA_PrecursorToMature(miRNANames)
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
miRNA_PrecursorToMature<-function(miRNANames,version=NULL)
{
if(is.null(version))
{
c_version=checkMiRNAVersion(miRNANames,verbose = FALSE)
cat(paste0("The input miRNA version information: miRBase ",c_version))
}
else
c_version=version
ver_index=match(tolower(c_version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
VMAP <-miRNA_data[[ver_index]][,c(2,6,9)]
VMAP[,1]=SYM[VMAP[,1]]
VMAP[,2]=SYM[VMAP[,2]]
VMAP[,3]=SYM[VMAP[,3]]
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
uid = unique(as.vector(miRNANames))
uid=na.omit(uid)
ind=apply(VMAP,2,function(x){match(uid,x)})
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),2]
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),3]
target <- data.frame(
OriginalName = uid,
Mature1 = VMAP[ind[,1],2],
Mature2 = VMAP[ind[,1],3],
row.names=NULL, stringsAsFactors = FALSE)
target=target[match(miRNANames, target$OriginalName),]
rownames(target)=NULL
target
}
#' Convert the mature miRNAs to the corresponding precursors
#'
#' This function converts the mature miRNAs to the corresponding precursors in the specified miRBase version.
#' @param miRNANames A character vector representing the miRNA names.
#' @param version The default is \strong{NULL} representing the most possible latest version of the input miRNA Names will be checked automatically.
#' Otherwise, a character value representing the version corresponding the input miRNA Names.
#' Users can apply the function \strong{getAllVersionInfo()} to get the available miRNA version names.
#' The optional values are in below:\cr
#' "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14",\cr
#' "v15","v16","v17","v18","v19","v20","v21","v22"\cr
#' @return
#' A data frame(nx2). The number of rows equal to the input miRNA Names. The two columns are defined as below:
#' \itemize{
#' \item \strong{OriginalName} : The input miRNA Names.\cr
#' \item \strong{Precursor} : The corresponding precursors of the mature miRNAs.\cr
#' }
#'
#' @examples
#' data(miRNATest)
#' miRNANames=miRNATest$miRNA_Name
#' result=miRNA_MatureToPrecursor(miRNANames)
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
miRNA_MatureToPrecursor<-function(miRNANames,version=NULL)
{
if(is.null(version))
{
c_version=rev(checkMiRNAVersion(miRNANames,verbose = FALSE))[1]
cat(paste0("The input miRNA version information: miRBase ",c_version))
}
else
c_version=version
ver_index=match(tolower(c_version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
VMAP <-miRNA_data[[ver_index]][,c(2,6,9)]
VMAP[,1]=SYM[VMAP[,1]]
VMAP[,2]=SYM[VMAP[,2]]
VMAP[,3]=SYM[VMAP[,3]]
miRNANames=as.character(miRNANames)
miRNANames=gsub(" ","",miRNANames)##Remove the possible space
uid = unique(as.vector(miRNANames))
uid=na.omit(uid)
ind=apply(VMAP,2,function(x){match(uid,x)})
ind[which(is.na(ind[,2])),2]=ind[which(is.na(ind[,2])),3]
ind[which(is.na(ind[,2])),2]=ind[which(is.na(ind[,2])),1]
target <- data.frame(
OriginalName = uid,
Precursor = VMAP[ind[,2],1],
row.names=NULL, stringsAsFactors = FALSE)
target=target[match(miRNANames, target$OriginalName),]
rownames(target)=NULL
target
}
#' Check the miRNA family
#'
#' This function checks the miRNA family for a list of miRNA Names.
#'
#' @param Accessions A character vector representing the miRNA Accessions in miRBase.
#' @examples
#' data(miRNATest)
#' ## The input is miRNA Accessions
#' Accessions=miRNATest$Accession
#' Family_Info1=checkMiRNAFamily(Accessions)
#'
#' ##The input is miRNA names
#' miRNANames=miRNATest$miRNA_Name
#' version=checkMiRNAVersion(miRNANames,verbose = TRUE)
#' result=miRNA_NameToAccession(miRNANames,version=version)
#' Accessions=result$Accession
#' Family_Info2=checkMiRNAFamily(Accessions)
#'
#' @return
#' A data frame with four columns. The number of rows equal to the input Accessions. The four columns are defined as below:
#' \itemize{
#' \item \strong{Accession} : The input miRNA accessions.\cr
#' \item \strong{miRNAName_v21} : The miRNA names (version 21) corresponding to the Accession.\cr
#' \item \strong{FamilyAccession} : The accession of the family .\cr
#' \item \strong{Family} : The family name.\cr
#' }
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
#'
checkMiRNAFamily<-function(Accessions)
{
Accessions=as.character(Accessions)
Accessions=gsub(" ","",Accessions)##Remove the possible space
uid=unique(as.vector(Accessions))
uid=na.omit(uid)
miRNANames=miRNA_AccessionToName(uid)
ACC_ID=match(uid,ACC)
#v21
VMAP <-miRNA_data[[21]][,c(1,5,8,12)]
ind=apply(VMAP,2,function(x){match(ACC_ID,x)})
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),2]
ind[which(is.na(ind[,1])),1]=ind[which(is.na(ind[,1])),3]
xx=FAM[VMAP$FAM[ind[,1]],]
target=data.frame(miRNANames,xx,stringsAsFactors=FALSE)
target=target[match(Accessions,target$Accession),]
rownames(target)=NULL
colnames(target)=c("Accession","miRNAName_v21","FamilyAccession","Family")
target
}
#' Open the miRNA family webpages of the specified miRNAs
#'
#' This function redirects the miRBase miRNA family webpages of the specified miRNA families
#'
#' @param FamilyAccessions A character vector representing the miRNA family Accessions in miRBase.
#' We restict the queried number of miRNA family each time. The maximum number of the input miRNA families is 15.
#' @param verbose Logical value. If true, the invalid miRNA Family will be printed the console.
#'
#' @examples
#' data(miRNATest)
#' Accessions=miRNATest$Accession
#' Family_Info=checkMiRNAFamily(Accessions)
#' FamilyAccessions=Family_Info$FamilyAccession[1:15]
#' goTo_miRNAFamily(FamilyAccessions)
#' @return
#' No values
#' @author
#' Xu, Taosheng \email{taosheng.x@@gmail.com}
#' @export
goTo_miRNAFamily<-function(FamilyAccessions, verbose = TRUE)
{
FamilyAccessions=unique(FamilyAccessions)
FamilyAccessions=na.omit(FamilyAccessions)
if(length(FamilyAccessions)>15)
{
message("The number of the queried miRNA familys is out of 15. Please reduce the input miRNA family number")
}
else
{
ind=match(FamilyAccessions,FAM$FAM_ACC)
ind1=which(is.na(ind))
ind2=which(!is.na(ind))
dead=FamilyAccessions[ind1]
alive=FamilyAccessions[ind2]
if(length(dead)>0 && verbose)
{
dead=data.frame("Invalid.miRNAFamily"=dead)
message("The invalid Family Accessions are in below: ")
print.data.frame(dead)
}
for(i in alive)
{
URL=paste0("http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=",i)
utils::browseURL(URL)
}
}
}
###internal function
.getmiRNAs<-function(version="v22")
{
ver_index=match(tolower(version),VER)
if (is.na(ver_index))
stop("It is a wrong version name, Please check it")
#MiRNAs <- as.matrix(miRNA_data[[ver_index]])
MiRNAs <- miRNA_data[[ver_index]]
Precursor=MiRNAs[,c(1,2,4)]
Mature1=MiRNAs[,c(5,6,7)]
Mature2=MiRNAs[,c(8,9,10)]
colnames(Precursor)=c("ACC","SYM","SEQ")
colnames(Mature1)=c("ACC","SYM","SEQ")
colnames(Mature2)=c("ACC","SYM","SEQ")
MiRNAs=rbind.data.frame(Precursor,Mature1,Mature2)
#MiRNAs=na.omit(MiRNAs)
##check the rows with all NA
ind <- which(apply(MiRNAs, 1, function(x) all(is.na(x))))
MiRNAs=MiRNAs[-ind,]
MiRNAs=unique(MiRNAs)
#MiRNAs=as.data.frame(MiRNAs,stringsAsFactors=FALSE)
MiRNAs
}
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