Nothing
lumiR.batch <- function(fileList, convertNuID = TRUE, lib.mapping = NULL, detectionTh = 0.01, QC = TRUE, transform = c('none', 'vst', 'log2', 'cubicRoot'), sampleInfoFile = NULL, verbose = TRUE, ...) {
oldDir <- getwd()
dirMode <- FALSE
transform <- match.arg(transform)
if (file.exists(fileList[1])) {
if (file.info(fileList[1])[1,'isdir']) {
dirMode <- TRUE
setwd(fileList)
}
}
if (dirMode && length(fileList) == 1) {
fileList <- dir(fileList, pattern='.csv')
if (length(fileList) == 0) stop('No data files were found!\n')
}
history.submitted <- as.character(Sys.time())
if (verbose) {
cat('Inputting the data ...\n')
if (transform != 'none') cat(paste('Transformation', transform, 'will be performed for each data file ...\n'))
}
for (i in 1:length(fileList)) {
file.i <- fileList[i]
if (transform != 'none') {
x.lumi.i <- lumiR(file.i, parseColumnName=FALSE, convertNuID = FALSE, verbose=FALSE, ...)
x.lumi.i <- lumiT(x.lumi.i, method=transform, simpleOutput=TRUE, verbose=FALSE)
} else {
x.lumi.i <- lumiR(file.i, parseColumnName=FALSE, convertNuID = FALSE, QC = FALSE, verbose=FALSE, ...)
}
if (i == 1) {
x.lumi <- x.lumi.i
} else {
x.lumi <- combine(x.lumi, x.lumi.i)
}
}
if (!convertNuID) lib.mapping <- NULL
if (!is.null(lib.mapping) || convertNuID) {
if (verbose) cat('\nAdding nuID to the data ...\n')
x.lumi <- addNuID2lumi(x.lumi, lib.mapping=lib.mapping)
}
if (!is.null(sampleInfoFile)) {
if (is.character(sampleInfoFile) || class(sampleInfoFile)[1] == 'file') {
if (file.exists(sampleInfoFile)) {
sampleInfo <- read.table(sampleInfoFile, header=TRUE, sep='\t', colClasses='character', comment.char='', check.names=FALSE)
} else {
warning('The provided sampleInfoFile does not exist\n!')
setwd(oldDir)
return(x.lumi)
}
} else if (is.data.frame(sampleInfoFile)) {
sampleInfo <- sampleInfoFile
}
## force the names to be capitalized
colName <- toupper(names(sampleInfo))
ind <- grep('ID$', colName, ignore.case=TRUE)
if (length(ind) == 0) {
ID <- sampleInfo[,1]
if (any(duplicated(ID))) {
warning('In sampleInfoFile, the ID column is required or the first column should be unique!\n')
setwd(oldDir)
return(x.lumi)
}
ind <- 1
} else {
ID <- sampleInfo[, ind[1]]
}
rownames(sampleInfo) <- ID
colnames(sampleInfo)[ind[1]] <- 'sampleID'
sampleName <- sampleNames(x.lumi)
ID <- ID[ID %in% sampleName]
if (nrow(sampleInfo) != length(ID)) {
warning('Some IDs provided in the sampleInfoFile do not exist the data file!\n')
if (length(ID) == 0) {
stop('The IDs provided in the sampleInfoFile do not match the data file!\n')
}
}
x.lumi <- x.lumi[, ID]
if (is.null(pData(phenoData(x.lumi)))) {
pData <- sampleInfo[ID,]
} else {
pData <- data.frame(pData(phenoData(x.lumi))[!(toupper(names(pData(phenoData(x.lumi)))) %in% c(toupper(names(sampleInfo)), 'ID', 'SAMPLEID'))], sampleInfo[ID,])
}
label <- sampleInfo[ID, colName == 'LABEL']
if (length(label) == length(ID)) {
rownames(pData) <- label
sampleNames(x.lumi) <- label
}
pdata <- new("AnnotatedDataFrame", data=pData)
phenoData(x.lumi) <- pdata
}
## ----------------------------------------
# Add history track
if (is(x.lumi, 'LumiBatch')) {
history.finished <- as.character(Sys.time())
# history.command <- capture.output(print(match.call(lumiR.batch)))
history.command <- paste(deparse(match.call(lumiR.batch)), collapse='')
## replace with the real file name
if (length(fileList) > 1) {
fileList <- paste('c("', paste(fileList, collapse='","', sep=''), '")', sep='')
} else {
fileList <- paste('"', fileList, '"', sep='')
}
if (length(grep(',', history.command)) > 0) {
history.command <- sub('\\(.+,', paste('(', fileList, ',', sep=''), history.command)
} else {
history.command <- sub('\\(.+\\)', paste('(', fileList, ')', sep=''), history.command)
}
lumiVersion <- packageDescription('lumi')$Version
x.lumi@history<- data.frame(submitted=history.submitted,
finished=history.finished, command=history.command, lumiVersion=lumiVersion)
}
## initialize the QC slot in the LumiBatch object
if (QC) x.lumi <- lumiQ(x.lumi, detectionTh=detectionTh, verbose=verbose)
setwd(oldDir)
return(x.lumi)
}
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