R/maser.R
In DiogoVeiga/maser: Mapping Alternative Splicing Events to pRoteins
Defines functions
.onAttach
create_stats
maser
create_GRanges
create_GRanges_MXE
create_GRanges_IR
create_GRanges_ES
create_GRanges_ASS
create_GRanges_exon
Documented in
maser
#' @importFrom GenomicRanges GRanges
#' @importFrom IRanges IRanges
create_GRanges_exon <- function(chr, start, end, strand, id, gene_id,
gene_symbol){
if(any(!grepl("chr", chr))){
echr <- paste0("chr", chr)
}else{
echr <- chr
}
exon <- GRanges(seqnames = echr,
ranges = IRanges::IRanges(start = start, end = end), strand = strand,
ID = id, GeneID = gene_id, geneSymbol = gene_symbol)
return(exon)
}
create_GRanges_ASS <- function(events){
exon_long <- create_GRanges_exon(events$chr, events$longExonStart_0base+1,
events$longExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_short <- create_GRanges_exon(events$chr, events$shortES+1, events$shortEE,
events$strand, events$ID, events$GeneID, events$geneSymbol)
exon_flanking <- create_GRanges_exon(events$chr, events$flankingES+1,
events$flankingEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_long" = exon_long, "exon_short" = exon_short,
"exon_flanking" = exon_flanking)
return(grl)
}
create_GRanges_ES <- function(events){
exon_target <- create_GRanges_exon(events$chr, events$exonStart_0base+1,
events$exonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_upstream <- create_GRanges_exon(events$chr, events$upstreamES+1,
events$upstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_downstream <- create_GRanges_exon(events$chr, events$downstreamES+1,
events$downstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_target" = exon_target,
"exon_upstream" = exon_upstream,
"exon_downstream" = exon_downstream)
return(grl)
}
create_GRanges_IR <- function(events){
exon_ir <- create_GRanges_exon(events$chr, events$riExonStart_0base+1,
events$riExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_upstream <- create_GRanges_exon(events$chr, events$upstreamES+1,
events$upstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_downstream <- create_GRanges_exon(events$chr, events$downstreamES+1,
events$downstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_ir" = exon_ir,
"exon_upstream" = exon_upstream,
"exon_downstream" = exon_downstream)
return(grl)
}
create_GRanges_MXE <- function(events){
exon1 <- create_GRanges_exon(events$chr, events$X1stExonStart_0base+1,
events$X1stExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon2 <- create_GRanges_exon(events$chr, events$X2ndExonStart_0base+1,
events$X2ndExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_upstream <- create_GRanges_exon(events$chr, events$upstreamES+1,
events$upstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_downstream <- create_GRanges_exon(events$chr, events$downstreamES+1,
events$downstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_1" = exon1, "exon_2" = exon2,
"exon_upstream" = exon_upstream,
"exon_downstream" = exon_downstream)
return(grl)
}
create_GRanges <- function(events, type){
if(type == "A3SS" || type == "A5SS") {
grl <- create_GRanges_ASS(events)
}
if (type == "SE"){
grl <- create_GRanges_ES(events)
}
if (type == "RI"){
grl <- create_GRanges_IR(events)
}
if (type == "MXE"){
grl <- create_GRanges_MXE(events)
}
return(grl)
}
#' Create a maser object by importing rMATS splicing events.
#'
#' @param path a character specifiying the folder containing rMATS output files.
#' @param cond_labels a character vector of length 2 describing labels for
#' experimental conditions.
#' @param ftype a character indicating the rMATS file type.
#' Possible values are \code{c("ReadsOnTargetAndJunctionCounts",
#' "JunctionCountOnly", "JCEC", "JC")}.
#' @return A maser object.
#' @details This function creates a maser object by importing rMATS output.
#' \code{ftype} indicates which rMATS files to import.
#' \code{ReadsOnTargetandJunction or JunctionCountOnly} are used in rMATS 3.2.5
#' or lower. Newer versions (>4.0.1) use \code{"JCEC" or "JC"} nomenclature.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' @export
#' @import methods
#' @importFrom utils read.table
maser <- function(path, cond_labels,
ftype = c("ReadsOnTargetAndJunctionCounts",
"JunctionCountOnly",
"JCEC", "JC")){
ftype <- match.arg(ftype)
rmats_out <- list.files(path, pattern = paste0(ftype, ".txt"),
full.names = FALSE)
mats <- new("Maser")
if(ftype == "ReadsOnTargetAndJunctionCounts"){
counts.col <- c("IC_SAMPLE_1", "IC_SAMPLE_2")
}else{
counts.col <- c("IJC_SAMPLE_1", "IJC_SAMPLE_2")
}
if(!grepl("/$", path)){
path <- paste0(path, "/")
}
# For each AS type
for (f in rmats_out) {
events <- read.table(paste0(path, f), sep = "\t",
stringsAsFactors = FALSE, header = TRUE)
type <- unlist(strsplit(f, ".", fixed = TRUE))[1]
# prepare read counts matrix
inc1 <- strsplit(events[ , counts.col[1]], ",")
inc2 <- strsplit(events[ , counts.col[2]], ",")
reads.inc1 <- suppressWarnings(matrix(as.numeric(unlist(inc1)),
nrow = length(inc1), ncol = length(inc1[[1]]), byrow = TRUE))
reads.inc2 <- suppressWarnings(matrix(as.numeric(unlist(inc2)),
nrow = length(inc2), ncol = length(inc2[[1]]), byrow = TRUE))
reads.mat <- cbind(reads.inc1, reads.inc2)
rownames(reads.mat) <- events$ID
col_names <- c(paste0(cond_labels[1], "_", seq(1, length(inc1[[1]]), 1)),
paste0(cond_labels[2], "_", seq(1, length(inc2[[1]]), 1)) )
colnames(reads.mat) <- col_names
slot(mats, paste0(type,"_","counts")) <- reads.mat
# prepare PSI matrix
inc1 <- strsplit(events[ , "IncLevel1"], ",")
inc2 <- strsplit(events[ , "IncLevel2"], ",")
reads.inc1 <- suppressWarnings(matrix(as.numeric(unlist(inc1)),
nrow = length(inc1), ncol = length(inc1[[1]]), byrow = TRUE))
reads.inc2 <- suppressWarnings(matrix(as.numeric(unlist(inc2)),
nrow = length(inc2), ncol = length(inc2[[1]]), byrow = TRUE))
reads.mat <- cbind(reads.inc1, reads.inc2)
rownames(reads.mat) <- events$ID
colnames(reads.mat) <- col_names
slot(mats, paste0(type,"_","PSI")) <- reads.mat
# Number of samples condition 1 and 2
mats@n_cond1 <- length(inc1[[1]])
mats@n_cond2 <- length(inc2[[1]])
mats@conditions <- cond_labels
# rMATS stats
slot(mats, paste0(type,"_","stats")) <-
events[ , c("ID", "PValue", "FDR", "IncLevelDifference")]
# Genomic ranges of alternative splicing events
grl <- create_GRanges(events, type)
slot(mats, paste0(type,"_","gr")) <- grl
# Event annotation
slot(mats, paste0(type,"_","events")) <-
events[ , c("ID", "GeneID", "geneSymbol")]
}
return(mats)
}
#' S4 class to represent splicing events imported from rMATS.
#'
setClass("Maser",
slots = list(A3SS_counts = "matrix", A3SS_PSI = "matrix",
A3SS_stats = "data.frame", A3SS_events = "data.frame",
A3SS_gr = "GRangesList",
A5SS_counts = "matrix", A5SS_PSI = "matrix",
A5SS_stats = "data.frame", A5SS_events = "data.frame",
A5SS_gr = "GRangesList",
SE_counts = "matrix", SE_PSI = "matrix",
SE_stats = "data.frame", SE_events = "data.frame",
SE_gr = "GRangesList",
RI_counts = "matrix", RI_PSI = "matrix",
RI_stats = "data.frame", RI_events = "data.frame",
RI_gr = "GRangesList",
MXE_counts = "matrix", MXE_PSI = "matrix",
MXE_stats = "data.frame", MXE_events = "data.frame",
MXE_gr = "GRangesList",
n_cond1 = "numeric",
n_cond2 = "numeric",
conditions = "character"
)
)
setValidity2("Maser", function(object){
if(!length(object@conditions) == 2){
return("'conditions' slot must be a character vector of size 2.")
}
TRUE
})
setMethod("show", "Maser", function(object){
as_types <- c("A3SS", "A5SS", "SE", "RI", "MXE")
total <- 0
line_events <- ""
nevents <- 0
lapply(as_types, function(type){
PSI <- slot(object, paste0(type,"_","PSI"))
nevents <- nrow(PSI)
line_events <<- paste0(line_events,
type, ".......... ", nevents, " events\n")
total <<- total + nevents
})
conditions <- slot(object, "conditions")
line1 <- paste0("A Maser object with ", total, " splicing events.\n\n")
line2 <- paste0("Samples description: \n", "Label=", conditions[1],
" n=", slot(object, "n_cond1"),
" replicates\n")
line3 <- paste0( "Label=", conditions[2], " n=", slot(object, "n_cond2"),
" replicates\n\n")
line4 <- paste0("Splicing events: \n")
cat(paste0(line1, line2, line3, line4, line_events))
})
setAs("Maser", "list", function(from){
mapply(function(y) {
#apply as.list if the slot is again an user-defined object
#therefore, as.list gets applied recursively
if (inherits(slot(from,y),"Maser")) {
as.list(slot(from,y))
} else {
#otherwise just return the slot
slot(from,y)
}
},
slotNames(class(from)),
SIMPLIFY=FALSE)
})
setAs("list", "Maser", function(from){
y <- new("Maser")
if (!any(names(from) %in% slotNames(y))){
return("Invalid slot names.")
}
lapply(names(from), function(aslot){
slot(y, paste0(aslot)) <<- from[[paste0(aslot)]]
})
return(y)
})
#' @import methods
create_stats <- function(events, type){
annot <- slot(events, paste0(type,"_","events"))
stats <- slot(events, paste0(type,"_","stats"))
PSI <- slot(events, paste0(type,"_","PSI"))
grl <- slot(events, paste0(type,"_","gr"))
df <- annot
df <- cbind(df, stats[,2:4])
idx.cond1 <- seq(1, events@n_cond1, 1)
idx.cond2 <- seq(events@n_cond1+1, events@n_cond1+events@n_cond2, 1)
PSI_1 <- vapply(seq_along(PSI[,1]), function(i){
paste(PSI[i, idx.cond1], collapse = ",")
}, character(1)
)
PSI_2 <- vapply(seq_along(PSI[,1]), function(i){
paste(PSI[i, idx.cond2], collapse = ",")
}, character(1)
)
df <- cbind(df, PSI_1 = PSI_1, PSI_2 = PSI_2)
exon_df <- data.frame(Chr = as.character(seqnames(grl[[1]])),
Strand = as.character(strand(grl[[1]])))
lapply(seq_along(grl), function(i){
res <- as.data.frame(grl[[i]])
coord <- paste0(res$start, "-", res$end)
exon_df <<- cbind(exon_df, Exon = coord)
})
colnames(exon_df) <- c("Chr", "Strand", names(grl))
df <- cbind(df, exon_df)
return(df)
}
#' Retrieve PSI (percent spliced in) values from a maser object.
#'
#' @param events a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a matrix.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(PSI(hypoxia, "SE"))
#' @export
#' @import methods
setGeneric("PSI", function(events, type) standardGeneric("PSI"))
#' Retrieve PSI (percent spliced in) values from a maser object.
#'
#' @param events a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a matrix.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(PSI(hypoxia, "SE"))
#' @export
#' @import methods
setMethod("PSI", signature(events="Maser", type="character"),
function(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(slot(events, paste0(type,"_","PSI")))
})
#' Retrieve raw read counts values from a maser object.
#'
#' @param object a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a matrix.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(counts(hypoxia, "SE"))
#' @export
#' @import methods
#' @importMethodsFrom BiocGenerics counts
setMethod("counts", "Maser",
function(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(slot(object, paste0(type,"_","counts")))
})
#' Retrieve annotation of splicing events from a maser object.
#'
#' @param object a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a data.frame.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(annotation(hypoxia, "SE"))
#' @export
#' @import methods
#' @importMethodsFrom BiocGenerics annotation
setMethod("annotation", "Maser",
function(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(slot(object, paste0(type,"_","events")))
})
#' Retrieve rMATS stats of differential splicing from a maser object.
#'
#' @param object a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a data.frame.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(summary(hypoxia, "SE"))
#' @export
#' @import methods
setMethod("summary", "Maser",
function(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(create_stats(object, type))
})
#' Retrieve genomic ranges of splicing events from a maser object.
#'
#' @param x a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @param ... additional arguments.
#' @return a GRangesList.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(granges(hypoxia, type = "SE"))
#' @import methods
setMethod("granges", "Maser",
function(x, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), ...) {
type <- match.arg(type)
return(slot(x, paste0(type,"_","gr")))
})
.onAttach <- function(libname, pkgname) {
packageStartupMessage("Welcome to maser")
}
DiogoVeiga/maser documentation built on Feb. 10, 2022, 10:10 a.m.
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Defines functions .onAttach create_stats maser create_GRanges create_GRanges_MXE create_GRanges_IR create_GRanges_ES create_GRanges_ASS create_GRanges_exon
Documented in maser
#' @importFrom GenomicRanges GRanges
#' @importFrom IRanges IRanges
create_GRanges_exon <- function(chr, start, end, strand, id, gene_id,
gene_symbol){
if(any(!grepl("chr", chr))){
echr <- paste0("chr", chr)
}else{
echr <- chr
}
exon <- GRanges(seqnames = echr,
ranges = IRanges::IRanges(start = start, end = end), strand = strand,
ID = id, GeneID = gene_id, geneSymbol = gene_symbol)
return(exon)
}
create_GRanges_ASS <- function(events){
exon_long <- create_GRanges_exon(events$chr, events$longExonStart_0base+1,
events$longExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_short <- create_GRanges_exon(events$chr, events$shortES+1, events$shortEE,
events$strand, events$ID, events$GeneID, events$geneSymbol)
exon_flanking <- create_GRanges_exon(events$chr, events$flankingES+1,
events$flankingEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_long" = exon_long, "exon_short" = exon_short,
"exon_flanking" = exon_flanking)
return(grl)
}
create_GRanges_ES <- function(events){
exon_target <- create_GRanges_exon(events$chr, events$exonStart_0base+1,
events$exonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_upstream <- create_GRanges_exon(events$chr, events$upstreamES+1,
events$upstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_downstream <- create_GRanges_exon(events$chr, events$downstreamES+1,
events$downstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_target" = exon_target,
"exon_upstream" = exon_upstream,
"exon_downstream" = exon_downstream)
return(grl)
}
create_GRanges_IR <- function(events){
exon_ir <- create_GRanges_exon(events$chr, events$riExonStart_0base+1,
events$riExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_upstream <- create_GRanges_exon(events$chr, events$upstreamES+1,
events$upstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_downstream <- create_GRanges_exon(events$chr, events$downstreamES+1,
events$downstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_ir" = exon_ir,
"exon_upstream" = exon_upstream,
"exon_downstream" = exon_downstream)
return(grl)
}
create_GRanges_MXE <- function(events){
exon1 <- create_GRanges_exon(events$chr, events$X1stExonStart_0base+1,
events$X1stExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon2 <- create_GRanges_exon(events$chr, events$X2ndExonStart_0base+1,
events$X2ndExonEnd, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_upstream <- create_GRanges_exon(events$chr, events$upstreamES+1,
events$upstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
exon_downstream <- create_GRanges_exon(events$chr, events$downstreamES+1,
events$downstreamEE, events$strand, events$ID, events$GeneID,
events$geneSymbol)
grl <- GRangesList("exon_1" = exon1, "exon_2" = exon2,
"exon_upstream" = exon_upstream,
"exon_downstream" = exon_downstream)
return(grl)
}
create_GRanges <- function(events, type){
if(type == "A3SS" || type == "A5SS") {
grl <- create_GRanges_ASS(events)
}
if (type == "SE"){
grl <- create_GRanges_ES(events)
}
if (type == "RI"){
grl <- create_GRanges_IR(events)
}
if (type == "MXE"){
grl <- create_GRanges_MXE(events)
}
return(grl)
}
#' Create a maser object by importing rMATS splicing events.
#'
#' @param path a character specifiying the folder containing rMATS output files.
#' @param cond_labels a character vector of length 2 describing labels for
#' experimental conditions.
#' @param ftype a character indicating the rMATS file type.
#' Possible values are \code{c("ReadsOnTargetAndJunctionCounts",
#' "JunctionCountOnly", "JCEC", "JC")}.
#' @return A maser object.
#' @details This function creates a maser object by importing rMATS output.
#' \code{ftype} indicates which rMATS files to import.
#' \code{ReadsOnTargetandJunction or JunctionCountOnly} are used in rMATS 3.2.5
#' or lower. Newer versions (>4.0.1) use \code{"JCEC" or "JC"} nomenclature.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' @export
#' @import methods
#' @importFrom utils read.table
maser <- function(path, cond_labels,
ftype = c("ReadsOnTargetAndJunctionCounts",
"JunctionCountOnly",
"JCEC", "JC")){
ftype <- match.arg(ftype)
rmats_out <- list.files(path, pattern = paste0(ftype, ".txt"),
full.names = FALSE)
mats <- new("Maser")
if(ftype == "ReadsOnTargetAndJunctionCounts"){
counts.col <- c("IC_SAMPLE_1", "IC_SAMPLE_2")
}else{
counts.col <- c("IJC_SAMPLE_1", "IJC_SAMPLE_2")
}
if(!grepl("/$", path)){
path <- paste0(path, "/")
}
# For each AS type
for (f in rmats_out) {
events <- read.table(paste0(path, f), sep = "\t",
stringsAsFactors = FALSE, header = TRUE)
type <- unlist(strsplit(f, ".", fixed = TRUE))[1]
# prepare read counts matrix
inc1 <- strsplit(events[ , counts.col[1]], ",")
inc2 <- strsplit(events[ , counts.col[2]], ",")
reads.inc1 <- suppressWarnings(matrix(as.numeric(unlist(inc1)),
nrow = length(inc1), ncol = length(inc1[[1]]), byrow = TRUE))
reads.inc2 <- suppressWarnings(matrix(as.numeric(unlist(inc2)),
nrow = length(inc2), ncol = length(inc2[[1]]), byrow = TRUE))
reads.mat <- cbind(reads.inc1, reads.inc2)
rownames(reads.mat) <- events$ID
col_names <- c(paste0(cond_labels[1], "_", seq(1, length(inc1[[1]]), 1)),
paste0(cond_labels[2], "_", seq(1, length(inc2[[1]]), 1)) )
colnames(reads.mat) <- col_names
slot(mats, paste0(type,"_","counts")) <- reads.mat
# prepare PSI matrix
inc1 <- strsplit(events[ , "IncLevel1"], ",")
inc2 <- strsplit(events[ , "IncLevel2"], ",")
reads.inc1 <- suppressWarnings(matrix(as.numeric(unlist(inc1)),
nrow = length(inc1), ncol = length(inc1[[1]]), byrow = TRUE))
reads.inc2 <- suppressWarnings(matrix(as.numeric(unlist(inc2)),
nrow = length(inc2), ncol = length(inc2[[1]]), byrow = TRUE))
reads.mat <- cbind(reads.inc1, reads.inc2)
rownames(reads.mat) <- events$ID
colnames(reads.mat) <- col_names
slot(mats, paste0(type,"_","PSI")) <- reads.mat
# Number of samples condition 1 and 2
mats@n_cond1 <- length(inc1[[1]])
mats@n_cond2 <- length(inc2[[1]])
mats@conditions <- cond_labels
# rMATS stats
slot(mats, paste0(type,"_","stats")) <-
events[ , c("ID", "PValue", "FDR", "IncLevelDifference")]
# Genomic ranges of alternative splicing events
grl <- create_GRanges(events, type)
slot(mats, paste0(type,"_","gr")) <- grl
# Event annotation
slot(mats, paste0(type,"_","events")) <-
events[ , c("ID", "GeneID", "geneSymbol")]
}
return(mats)
}
#' S4 class to represent splicing events imported from rMATS.
#'
setClass("Maser",
slots = list(A3SS_counts = "matrix", A3SS_PSI = "matrix",
A3SS_stats = "data.frame", A3SS_events = "data.frame",
A3SS_gr = "GRangesList",
A5SS_counts = "matrix", A5SS_PSI = "matrix",
A5SS_stats = "data.frame", A5SS_events = "data.frame",
A5SS_gr = "GRangesList",
SE_counts = "matrix", SE_PSI = "matrix",
SE_stats = "data.frame", SE_events = "data.frame",
SE_gr = "GRangesList",
RI_counts = "matrix", RI_PSI = "matrix",
RI_stats = "data.frame", RI_events = "data.frame",
RI_gr = "GRangesList",
MXE_counts = "matrix", MXE_PSI = "matrix",
MXE_stats = "data.frame", MXE_events = "data.frame",
MXE_gr = "GRangesList",
n_cond1 = "numeric",
n_cond2 = "numeric",
conditions = "character"
)
)
setValidity2("Maser", function(object){
if(!length(object@conditions) == 2){
return("'conditions' slot must be a character vector of size 2.")
}
TRUE
})
setMethod("show", "Maser", function(object){
as_types <- c("A3SS", "A5SS", "SE", "RI", "MXE")
total <- 0
line_events <- ""
nevents <- 0
lapply(as_types, function(type){
PSI <- slot(object, paste0(type,"_","PSI"))
nevents <- nrow(PSI)
line_events <<- paste0(line_events,
type, ".......... ", nevents, " events\n")
total <<- total + nevents
})
conditions <- slot(object, "conditions")
line1 <- paste0("A Maser object with ", total, " splicing events.\n\n")
line2 <- paste0("Samples description: \n", "Label=", conditions[1],
" n=", slot(object, "n_cond1"),
" replicates\n")
line3 <- paste0( "Label=", conditions[2], " n=", slot(object, "n_cond2"),
" replicates\n\n")
line4 <- paste0("Splicing events: \n")
cat(paste0(line1, line2, line3, line4, line_events))
})
setAs("Maser", "list", function(from){
mapply(function(y) {
#apply as.list if the slot is again an user-defined object
#therefore, as.list gets applied recursively
if (inherits(slot(from,y),"Maser")) {
as.list(slot(from,y))
} else {
#otherwise just return the slot
slot(from,y)
}
},
slotNames(class(from)),
SIMPLIFY=FALSE)
})
setAs("list", "Maser", function(from){
y <- new("Maser")
if (!any(names(from) %in% slotNames(y))){
return("Invalid slot names.")
}
lapply(names(from), function(aslot){
slot(y, paste0(aslot)) <<- from[[paste0(aslot)]]
})
return(y)
})
#' @import methods
create_stats <- function(events, type){
annot <- slot(events, paste0(type,"_","events"))
stats <- slot(events, paste0(type,"_","stats"))
PSI <- slot(events, paste0(type,"_","PSI"))
grl <- slot(events, paste0(type,"_","gr"))
df <- annot
df <- cbind(df, stats[,2:4])
idx.cond1 <- seq(1, events@n_cond1, 1)
idx.cond2 <- seq(events@n_cond1+1, events@n_cond1+events@n_cond2, 1)
PSI_1 <- vapply(seq_along(PSI[,1]), function(i){
paste(PSI[i, idx.cond1], collapse = ",")
}, character(1)
)
PSI_2 <- vapply(seq_along(PSI[,1]), function(i){
paste(PSI[i, idx.cond2], collapse = ",")
}, character(1)
)
df <- cbind(df, PSI_1 = PSI_1, PSI_2 = PSI_2)
exon_df <- data.frame(Chr = as.character(seqnames(grl[[1]])),
Strand = as.character(strand(grl[[1]])))
lapply(seq_along(grl), function(i){
res <- as.data.frame(grl[[i]])
coord <- paste0(res$start, "-", res$end)
exon_df <<- cbind(exon_df, Exon = coord)
})
colnames(exon_df) <- c("Chr", "Strand", names(grl))
df <- cbind(df, exon_df)
return(df)
}
#' Retrieve PSI (percent spliced in) values from a maser object.
#'
#' @param events a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a matrix.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(PSI(hypoxia, "SE"))
#' @export
#' @import methods
setGeneric("PSI", function(events, type) standardGeneric("PSI"))
#' Retrieve PSI (percent spliced in) values from a maser object.
#'
#' @param events a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a matrix.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(PSI(hypoxia, "SE"))
#' @export
#' @import methods
setMethod("PSI", signature(events="Maser", type="character"),
function(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(slot(events, paste0(type,"_","PSI")))
})
#' Retrieve raw read counts values from a maser object.
#'
#' @param object a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a matrix.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(counts(hypoxia, "SE"))
#' @export
#' @import methods
#' @importMethodsFrom BiocGenerics counts
setMethod("counts", "Maser",
function(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(slot(object, paste0(type,"_","counts")))
})
#' Retrieve annotation of splicing events from a maser object.
#'
#' @param object a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a data.frame.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(annotation(hypoxia, "SE"))
#' @export
#' @import methods
#' @importMethodsFrom BiocGenerics annotation
setMethod("annotation", "Maser",
function(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(slot(object, paste0(type,"_","events")))
})
#' Retrieve rMATS stats of differential splicing from a maser object.
#'
#' @param object a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @return a data.frame.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(summary(hypoxia, "SE"))
#' @export
#' @import methods
setMethod("summary", "Maser",
function(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE")) {
type <- match.arg(type)
return(create_stats(object, type))
})
#' Retrieve genomic ranges of splicing events from a maser object.
#'
#' @param x a maser object.
#' @param type a character indicating the splice type. Possible values
#' are \code{c("A3SS", "A5SS", "SE", "RI", "MXE")}.
#' @param ... additional arguments.
#' @return a GRangesList.
#' @examples
#' path <- system.file("extdata", file.path("MATS_output"), package = "maser")
#' hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
#' head(granges(hypoxia, type = "SE"))
#' @import methods
setMethod("granges", "Maser",
function(x, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), ...) {
type <- match.arg(type)
return(slot(x, paste0(type,"_","gr")))
})
.onAttach <- function(libname, pkgname) {
packageStartupMessage("Welcome to maser")
}
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