R/createSampleListFunction.R
In hanielcedraz/baqcomPackage: Functions for BAQCOM pipeline
Defines functions
createSampleList
Documented in
createSampleList
#' @export
#' @name createSampleList
#' @title Creating sample list to run mcapply parallel
#' @author Haniel Cedraz
#' @details December 2021
#' @usage
#' createSampleList(samples, reads_folder, column, program, libraryType, fileType, fromSTAR = FALSE)
#' @description
#' Function to create sample list to run mcapply parallel
#'
#' @param samples
#' \code{Character.} The filename of the sample file. Default samples.txt.
#' @param reads_folder
#' \code{Character.} Directory where the raw sequence data is stored. Default 00-Fastq.
#' @param column
#' \code{Character.} Column name from the sample sheet to use as read folder names. Default SAMPLE_ID
#' @param program
#' \code{Character.} The program to be used. Available 'trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools' or 'bwa'
#' @param libraryType
#' \code{Character.} The library type to use. Available: 'pairEnd' or 'singleEnd'.
#' @param fileType
#' \code{Character.} The file type to use. Available: 'bam' or 'sam'.
#' @param fromSTAR
#' \code{Logical.} Wheter to use samples from STAR in FeatureCouts
#' @importFrom glue glue
#' @export
#reads_folder <- "/Users/haniel/OneDrive/posDoc/miRbaqcom/01-CleanedReadsReal/"
createSampleList <- function(samples, reads_folder, column, program, libraryType, fileType = NULL, fromSTAR = FALSE) {
samples <- as.data.frame(samples)
aceptedFileTypes <- c("bam", "sam", "fastq.gz")
if (!is.null(fileType)){
if (!fileType %in% aceptedFileTypes) {
stop(glue("File type ({fileType}) not found, please provide one of 'bam' or 'sam' "))
}
}
aceptedPrograms <- c('trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools', 'bwa')
if (!program %in% aceptedPrograms) {
stop(glue("Program ({program}) not found, please provide one of 'trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools' or 'bwa'"))
}
aceptedLibraryType <- c("pairEnd", "singleEnd")
if (!libraryType %in% aceptedLibraryType) {
stop(glue("Library type ({libraryType}) not found, please provide one of 'pairEnd' or 'singleEnd'"))
}
if (!file.exists(reads_folder)) {
stop(glue("reads_folder {reads_folder} does not exist\n"))
}
### column SAMPLE_ID should be the sample name
### rows can be commented out with #
if (libraryType == "pairEnd") {
if (!all(c(column, "Read_1", "Read_2") %in% colnames(samples))) {
stop(glue("Expecting the three columns {column}, Read_1 and Read_2 in samples file (tab-delimited)\n"))
}
}
if (program == "trimmomatic") {
if (libraryType == "pairEnd") {
#qcList <- function(samples, reads_folder, column){
mapping_list <- list()
for (i in 1:nrow(samples)) {
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
#reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
map <- lapply(c("_R1","_R2"), grep, x = reads, value = TRUE)
names(map) <- c("R1","R2")
map$sampleName <- samples[i,column]
map$R1 <- samples[i,2]
map$R2 <- samples[i,3]
mapping_list[[paste(map$sampleName)]] <- map
#mapping_list[[paste(map$sampleName)]]
}
write(paste("Setting up",length(mapping_list),"jobs"), stdout())
return(mapping_list)
#}
} else if (libraryType == "singleEnd") {
#qcList <- function(samples, reads_folder, column){
mapping_list <- list()
# samples <- read.table("samplesSingle.txt", header = TRUE)
# reads_folder <- "00-FastqSingle/"
# column <- "SAMPLE_ID"
for (i in 1:nrow(samples)) {
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
#reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
names(map) <- c("SE")
map$sampleName <- samples[i,column]
#map$SE <- map$SE[i]
map$SE <- map$SE[i]
mapping_list[[paste(map$sampleName)]] <- map
#mapping_list[[paste(map$sampleName)]]
}
write(paste("Setting up",length(mapping_list),"jobs"), stdout())
return(mapping_list)
#}
}
} else if (program == "star" | program == "Hisat2" | program == "bowtie" | program == "bwa") {
if (libraryType == "pairEnd") {
#mappingList <- function(samples, reads_folder, column){
mapping_list <- list()
for (i in 1:nrow(samples)) {
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
if (program == "bowtie") {
reads <- dir(path = file.path(reads_folder), pattern = "fastq$", full.names = TRUE)
}
# for (i in seq.int(to=nrow(samples))){
# reads <- dir(path=file.path(reads_folder,samples[i,column]),pattern="gz$",full.names=TRUE)
map <- lapply(c("_PE1", "_PE2", "_SE1", "_SE2"), grep, x = reads, value = TRUE)
names(map) <- c("PE1", "PE2", "SE1", "SE2")
map$sampleName <- samples[i,column]
map$PE1 <- map$PE1[i]
map$PE2 <- map$PE2[i]
map$SE1 <- map$SE1[i]
map$SE2 <- map$SE2[i]
mapping_list[[paste(map$sampleName)]] <- map
mapping_list[[paste(map$sampleName, sep = "_")]]
}
write(paste("Setting up", length(mapping_list), "jobs"),stdout())
return(mapping_list)
#}
} else if (libraryType == "singleEnd") {
#mappingList <- function(samples, reads_folder, column){
mapping_list <- list()
for (i in 1:nrow(samples)) {
#reads_folder <- "01-CleanedReadsSingle/"
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
if (program == "bowtie") {
reads <- dir(path = file.path(reads_folder), pattern = "fastq$", full.names = TRUE)
}
#reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
names(map) <- c("SE")
map$sampleName <- samples[i,column]
map$SE <- map$SE[i]
#map$R2 <- samples[i,3]
mapping_list[[paste(map$sampleName)]] <- map
#mapping_list[[paste(map$sampleName)]]
}
write(paste("Setting up",length(mapping_list),"jobs"), stdout())
return(mapping_list)
#}
}
} else if (program == "htseq") {
counting_list <- list()
if (casefold(fileType, upper = FALSE) == 'bam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.bam$'), full.names = TRUE)
count <- lapply(c("_sam_sorted_pos.bam"), grep, x = files, value = TRUE)
names(count) <- c("bam_sorted_pos")
count$sampleName <- samples[i,column]
count$bam_sorted_pos <- count$bam_sorted_pos[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
} else if (casefold(fileType, upper = FALSE) == 'sam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.sam$'), full.names = TRUE)
count <- lapply(c("_unsorted_sample.sam"), grep, x = files, value = TRUE)
names(count) <- c("unsorted_sample")
count$sampleName <- samples[i,column]
count$unsorted_sample <- count$unsorted_sample[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
}
write(paste("Setting up", length(counting_list), "jobs"),stdout())
return(counting_list)
} else if (program == "featurecount") {
if (fromSTAR) {
#reads_folder <- opt$inputFolder
#countingList <- function(samples, reads_folder, column) {
counting_list <- list()
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.bam$'), full.names = TRUE)
count <- lapply(c("_Aligned.sortedByCoord.out.bam"), grep, x = files, value = TRUE)
names(count) <- c("Aligned.sortedByCoord.out")
count$sampleName <- samples[i,column]
count$Aligned.sortedByCoord.out <- count$Aligned.sortedByCoord.out[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
write(paste("Setting up", length(counting_list), "jobs"),stdout())
return(counting_list)
#}
} else {
#countingList <- function(samples, reads_folder, column) {
counting_list <- list()
if (casefold(fileType, upper = FALSE) == 'bam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.bam$'), full.names = TRUE)
count <- lapply(c("_sam_sorted_pos.bam"), grep, x = files, value = TRUE)
names(count) <- c("bam_sorted_pos")
count$sampleName <- samples[i,column]
count$bam_sorted_pos <- count$bam_sorted_pos[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
} else if (casefold(fileType, upper = FALSE) == 'sam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.sam$'), full.names = TRUE)
count <- lapply(c("_unsorted_sample.sam"), grep, x = files, value = TRUE)
names(count) <- c("unsorted_sample")
count$sampleName <- samples[i,column]
count$unsorted_sample <- count$unsorted_sample[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
}
write(paste("Setting up", length(counting_list), "jobs"),stdout())
return(counting_list)
#}
}
} else if (program == "samtools") {
#samtoolsList <- function(samples, reads_folder, column){
samtoolsfiles <- list()
for (i in 1:nrow(samples)) {
samfiles <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = ".sam$", full.names = TRUE)
maps <- lapply(c("_unsorted_sample"), grep, x = samfiles, value = TRUE)
names(maps) <- c("unsorted_sample")
maps$sampleName <- samples[i,column]
maps$unsorted_sample <- maps$unsorted_sample[i]
samtoolsfiles[[paste(maps$sampleName)]] <- maps
samtoolsfiles[[paste(maps$sampleName, sep = "_")]]
}
write(paste("Setting up", length(samtoolsfiles), "jobs"),stdout())
return(samtoolsfiles)
#}
}
}
# else if (program == "bowtie") {
# if (libraryType == "pairEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_R1","_R2"), grep, x = reads, value = TRUE)
# names(map) <- c("R1","R2")
# map$sampleName <- samples[i,column]
# map$R1 <- samples[i,2]
# map$R2 <- samples[i,3]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# } else if (libraryType == "singleEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
# names(map) <- c("SE")
# map$sampleName <- samples[i,column]
# #map$SE <- map$SE[i]
# map$SE <- samples[i,2]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# }
# } # else if (program == "Hisat2") {
# if (libraryType == "pairEnd") {
# mappingList <- function(samples, reads_folder, column){
# mapping_list <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# # for (i in seq.int(to=nrow(samples))){
# # reads <- dir(path=file.path(reads_folder,samples[i,column]),pattern="gz$",full.names=TRUE)
# map <- lapply(c("_PE1", "_PE2", "_SE1", "_SE2"), grep, x = reads, value = TRUE)
# names(map) <- c("PE1", "PE2", "SE1", "SE2")
# map$sampleName <- samples[i,column]
# map$PE1 <- map$PE1[i]
# map$PE2 <- map$PE2[i]
# map$SE1 <- map$SE1[i]
# map$SE2 <- map$SE2[i]
# mapping_list[[paste(map$sampleName)]] <- map
# mapping_list[[paste(map$sampleName, sep = "_")]]
# }
# write(paste("Setting up", length(mapping_list), "jobs"),stdout())
# return(mapping_list)
# }
#
# } else if (libraryType == "singleEnd") {
# mappingList <- function(samples, reads_folder, column){
# mapping_list <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
# names(map) <- c("SE")
# map$sampleName <- samples[i,column]
# map$SE <- map$SE[i]
# #map$R2 <- samples[i,3]
# mapping_list[[paste(map$sampleName)]] <- map
# #mapping_list[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(mapping_list),"jobs"), stdout())
# return(mapping_list)
# }
# }
# }
#
#
#
#
#
#
#
#
#
# if (fileType == "fastq.gz") {
# if (libraryType == "pairEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_R1","_R2"), grep, x = reads, value = TRUE)
# names(map) <- c("R1","R2")
# map$sampleName <- samples[i,column]
# map$R1 <- samples[i,2]
# map$R2 <- samples[i,3]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# } else if (libraryType == "singleEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
# names(map) <- c("SE")
# map$sampleName <- samples[i,column]
# #map$SE <- map$SE[i]
# map$SE <- samples[i,2]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# }
#
# } else if (fileType == "bam") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "bam$", full.names = TRUE)
# map <- lapply(c(".bam"), grep, x = reads, value = TRUE)
# names(map) <- c("bam")
# map$sampleName <- samples[i,column]
# map$bam_sorted_pos <- map$bam[i]
#
# sampleList[[paste(map$sampleName)]] <- map
# sampleList[[paste(map$sampleName, sep = "_")]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
#
# } else if (fileType == "sam") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "sam$", full.names = TRUE)
# map <- lapply(c(".sam"), grep, x = reads, value = TRUE)
# names(map) <- c("sam")
# map$sampleName <- samples[i,column]
# map$bam_sorted_pos <- map$bam[i]
#
# sampleList[[paste(map$sampleName)]] <- map
# sampleList[[paste(map$sampleName, sep = "_")]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# }
#}
hanielcedraz/baqcomPackage documentation built on June 14, 2022, 12:25 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions createSampleList
Documented in createSampleList
#' @export
#' @name createSampleList
#' @title Creating sample list to run mcapply parallel
#' @author Haniel Cedraz
#' @details December 2021
#' @usage
#' createSampleList(samples, reads_folder, column, program, libraryType, fileType, fromSTAR = FALSE)
#' @description
#' Function to create sample list to run mcapply parallel
#'
#' @param samples
#' \code{Character.} The filename of the sample file. Default samples.txt.
#' @param reads_folder
#' \code{Character.} Directory where the raw sequence data is stored. Default 00-Fastq.
#' @param column
#' \code{Character.} Column name from the sample sheet to use as read folder names. Default SAMPLE_ID
#' @param program
#' \code{Character.} The program to be used. Available 'trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools' or 'bwa'
#' @param libraryType
#' \code{Character.} The library type to use. Available: 'pairEnd' or 'singleEnd'.
#' @param fileType
#' \code{Character.} The file type to use. Available: 'bam' or 'sam'.
#' @param fromSTAR
#' \code{Logical.} Wheter to use samples from STAR in FeatureCouts
#' @importFrom glue glue
#' @export
#reads_folder <- "/Users/haniel/OneDrive/posDoc/miRbaqcom/01-CleanedReadsReal/"
createSampleList <- function(samples, reads_folder, column, program, libraryType, fileType = NULL, fromSTAR = FALSE) {
samples <- as.data.frame(samples)
aceptedFileTypes <- c("bam", "sam", "fastq.gz")
if (!is.null(fileType)){
if (!fileType %in% aceptedFileTypes) {
stop(glue("File type ({fileType}) not found, please provide one of 'bam' or 'sam' "))
}
}
aceptedPrograms <- c('trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools', 'bwa')
if (!program %in% aceptedPrograms) {
stop(glue("Program ({program}) not found, please provide one of 'trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools' or 'bwa'"))
}
aceptedLibraryType <- c("pairEnd", "singleEnd")
if (!libraryType %in% aceptedLibraryType) {
stop(glue("Library type ({libraryType}) not found, please provide one of 'pairEnd' or 'singleEnd'"))
}
if (!file.exists(reads_folder)) {
stop(glue("reads_folder {reads_folder} does not exist\n"))
}
### column SAMPLE_ID should be the sample name
### rows can be commented out with #
if (libraryType == "pairEnd") {
if (!all(c(column, "Read_1", "Read_2") %in% colnames(samples))) {
stop(glue("Expecting the three columns {column}, Read_1 and Read_2 in samples file (tab-delimited)\n"))
}
}
if (program == "trimmomatic") {
if (libraryType == "pairEnd") {
#qcList <- function(samples, reads_folder, column){
mapping_list <- list()
for (i in 1:nrow(samples)) {
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
#reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
map <- lapply(c("_R1","_R2"), grep, x = reads, value = TRUE)
names(map) <- c("R1","R2")
map$sampleName <- samples[i,column]
map$R1 <- samples[i,2]
map$R2 <- samples[i,3]
mapping_list[[paste(map$sampleName)]] <- map
#mapping_list[[paste(map$sampleName)]]
}
write(paste("Setting up",length(mapping_list),"jobs"), stdout())
return(mapping_list)
#}
} else if (libraryType == "singleEnd") {
#qcList <- function(samples, reads_folder, column){
mapping_list <- list()
# samples <- read.table("samplesSingle.txt", header = TRUE)
# reads_folder <- "00-FastqSingle/"
# column <- "SAMPLE_ID"
for (i in 1:nrow(samples)) {
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
#reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
names(map) <- c("SE")
map$sampleName <- samples[i,column]
#map$SE <- map$SE[i]
map$SE <- map$SE[i]
mapping_list[[paste(map$sampleName)]] <- map
#mapping_list[[paste(map$sampleName)]]
}
write(paste("Setting up",length(mapping_list),"jobs"), stdout())
return(mapping_list)
#}
}
} else if (program == "star" | program == "Hisat2" | program == "bowtie" | program == "bwa") {
if (libraryType == "pairEnd") {
#mappingList <- function(samples, reads_folder, column){
mapping_list <- list()
for (i in 1:nrow(samples)) {
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
if (program == "bowtie") {
reads <- dir(path = file.path(reads_folder), pattern = "fastq$", full.names = TRUE)
}
# for (i in seq.int(to=nrow(samples))){
# reads <- dir(path=file.path(reads_folder,samples[i,column]),pattern="gz$",full.names=TRUE)
map <- lapply(c("_PE1", "_PE2", "_SE1", "_SE2"), grep, x = reads, value = TRUE)
names(map) <- c("PE1", "PE2", "SE1", "SE2")
map$sampleName <- samples[i,column]
map$PE1 <- map$PE1[i]
map$PE2 <- map$PE2[i]
map$SE1 <- map$SE1[i]
map$SE2 <- map$SE2[i]
mapping_list[[paste(map$sampleName)]] <- map
mapping_list[[paste(map$sampleName, sep = "_")]]
}
write(paste("Setting up", length(mapping_list), "jobs"),stdout())
return(mapping_list)
#}
} else if (libraryType == "singleEnd") {
#mappingList <- function(samples, reads_folder, column){
mapping_list <- list()
for (i in 1:nrow(samples)) {
#reads_folder <- "01-CleanedReadsSingle/"
reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
if (program == "bowtie") {
reads <- dir(path = file.path(reads_folder), pattern = "fastq$", full.names = TRUE)
}
#reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
names(map) <- c("SE")
map$sampleName <- samples[i,column]
map$SE <- map$SE[i]
#map$R2 <- samples[i,3]
mapping_list[[paste(map$sampleName)]] <- map
#mapping_list[[paste(map$sampleName)]]
}
write(paste("Setting up",length(mapping_list),"jobs"), stdout())
return(mapping_list)
#}
}
} else if (program == "htseq") {
counting_list <- list()
if (casefold(fileType, upper = FALSE) == 'bam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.bam$'), full.names = TRUE)
count <- lapply(c("_sam_sorted_pos.bam"), grep, x = files, value = TRUE)
names(count) <- c("bam_sorted_pos")
count$sampleName <- samples[i,column]
count$bam_sorted_pos <- count$bam_sorted_pos[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
} else if (casefold(fileType, upper = FALSE) == 'sam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.sam$'), full.names = TRUE)
count <- lapply(c("_unsorted_sample.sam"), grep, x = files, value = TRUE)
names(count) <- c("unsorted_sample")
count$sampleName <- samples[i,column]
count$unsorted_sample <- count$unsorted_sample[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
}
write(paste("Setting up", length(counting_list), "jobs"),stdout())
return(counting_list)
} else if (program == "featurecount") {
if (fromSTAR) {
#reads_folder <- opt$inputFolder
#countingList <- function(samples, reads_folder, column) {
counting_list <- list()
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.bam$'), full.names = TRUE)
count <- lapply(c("_Aligned.sortedByCoord.out.bam"), grep, x = files, value = TRUE)
names(count) <- c("Aligned.sortedByCoord.out")
count$sampleName <- samples[i,column]
count$Aligned.sortedByCoord.out <- count$Aligned.sortedByCoord.out[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
write(paste("Setting up", length(counting_list), "jobs"),stdout())
return(counting_list)
#}
} else {
#countingList <- function(samples, reads_folder, column) {
counting_list <- list()
if (casefold(fileType, upper = FALSE) == 'bam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.bam$'), full.names = TRUE)
count <- lapply(c("_sam_sorted_pos.bam"), grep, x = files, value = TRUE)
names(count) <- c("bam_sorted_pos")
count$sampleName <- samples[i,column]
count$bam_sorted_pos <- count$bam_sorted_pos[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
} else if (casefold(fileType, upper = FALSE) == 'sam') {
for (i in 1:nrow(samples)) {
files <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = paste0('.sam$'), full.names = TRUE)
count <- lapply(c("_unsorted_sample.sam"), grep, x = files, value = TRUE)
names(count) <- c("unsorted_sample")
count$sampleName <- samples[i,column]
count$unsorted_sample <- count$unsorted_sample[i]
counting_list[[paste(count$sampleName)]] <- count
counting_list[[paste(count$sampleName, sep = "_")]]
}
}
write(paste("Setting up", length(counting_list), "jobs"),stdout())
return(counting_list)
#}
}
} else if (program == "samtools") {
#samtoolsList <- function(samples, reads_folder, column){
samtoolsfiles <- list()
for (i in 1:nrow(samples)) {
samfiles <- dir(path = file.path(reads_folder), recursive = TRUE, pattern = ".sam$", full.names = TRUE)
maps <- lapply(c("_unsorted_sample"), grep, x = samfiles, value = TRUE)
names(maps) <- c("unsorted_sample")
maps$sampleName <- samples[i,column]
maps$unsorted_sample <- maps$unsorted_sample[i]
samtoolsfiles[[paste(maps$sampleName)]] <- maps
samtoolsfiles[[paste(maps$sampleName, sep = "_")]]
}
write(paste("Setting up", length(samtoolsfiles), "jobs"),stdout())
return(samtoolsfiles)
#}
}
}
# else if (program == "bowtie") {
# if (libraryType == "pairEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_R1","_R2"), grep, x = reads, value = TRUE)
# names(map) <- c("R1","R2")
# map$sampleName <- samples[i,column]
# map$R1 <- samples[i,2]
# map$R2 <- samples[i,3]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# } else if (libraryType == "singleEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
# names(map) <- c("SE")
# map$sampleName <- samples[i,column]
# #map$SE <- map$SE[i]
# map$SE <- samples[i,2]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# }
# } # else if (program == "Hisat2") {
# if (libraryType == "pairEnd") {
# mappingList <- function(samples, reads_folder, column){
# mapping_list <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# # for (i in seq.int(to=nrow(samples))){
# # reads <- dir(path=file.path(reads_folder,samples[i,column]),pattern="gz$",full.names=TRUE)
# map <- lapply(c("_PE1", "_PE2", "_SE1", "_SE2"), grep, x = reads, value = TRUE)
# names(map) <- c("PE1", "PE2", "SE1", "SE2")
# map$sampleName <- samples[i,column]
# map$PE1 <- map$PE1[i]
# map$PE2 <- map$PE2[i]
# map$SE1 <- map$SE1[i]
# map$SE2 <- map$SE2[i]
# mapping_list[[paste(map$sampleName)]] <- map
# mapping_list[[paste(map$sampleName, sep = "_")]]
# }
# write(paste("Setting up", length(mapping_list), "jobs"),stdout())
# return(mapping_list)
# }
#
# } else if (libraryType == "singleEnd") {
# mappingList <- function(samples, reads_folder, column){
# mapping_list <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
# names(map) <- c("SE")
# map$sampleName <- samples[i,column]
# map$SE <- map$SE[i]
# #map$R2 <- samples[i,3]
# mapping_list[[paste(map$sampleName)]] <- map
# #mapping_list[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(mapping_list),"jobs"), stdout())
# return(mapping_list)
# }
# }
# }
#
#
#
#
#
#
#
#
#
# if (fileType == "fastq.gz") {
# if (libraryType == "pairEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_R1","_R2"), grep, x = reads, value = TRUE)
# names(map) <- c("R1","R2")
# map$sampleName <- samples[i,column]
# map$R1 <- samples[i,2]
# map$R2 <- samples[i,3]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# } else if (libraryType == "singleEnd") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "fastq.gz$", full.names = TRUE)
# #reads <- dir(path=file.path(reads_folder, samples[i,column]), pattern = "fastq.gz$", full.names = TRUE)
# map <- lapply(c("_SE"), grep, x = reads, value = TRUE)
# names(map) <- c("SE")
# map$sampleName <- samples[i,column]
# #map$SE <- map$SE[i]
# map$SE <- samples[i,2]
# sampleList[[paste(map$sampleName)]] <- map
# #sampleList[[paste(map$sampleName)]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# }
#
# } else if (fileType == "bam") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "bam$", full.names = TRUE)
# map <- lapply(c(".bam"), grep, x = reads, value = TRUE)
# names(map) <- c("bam")
# map$sampleName <- samples[i,column]
# map$bam_sorted_pos <- map$bam[i]
#
# sampleList[[paste(map$sampleName)]] <- map
# sampleList[[paste(map$sampleName, sep = "_")]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
#
# } else if (fileType == "sam") {
# sampleList <- list()
# for (i in 1:nrow(samples)) {
# reads <- dir(path = file.path(reads_folder), pattern = "sam$", full.names = TRUE)
# map <- lapply(c(".sam"), grep, x = reads, value = TRUE)
# names(map) <- c("sam")
# map$sampleName <- samples[i,column]
# map$bam_sorted_pos <- map$bam[i]
#
# sampleList[[paste(map$sampleName)]] <- map
# sampleList[[paste(map$sampleName, sep = "_")]]
# }
# write(paste("Setting up",length(sampleList),"jobs"), stdout())
# return(sampleList)
# }
#}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.