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minfiFuncs.R
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minfiFuncs.R
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require(illuminaio)
read.450k.sheet <- function (base, pattern = "csv$", ignore.case = TRUE, recursive = TRUE,
verbose = TRUE)
{
readSheet <- function(file) {
dataheader <- grep("^\\[Data\\]", readLines(file))
if (length(dataheader) == 0)
dataheader <- 0
df <- read.csv(file, stringsAsFactor = FALSE, skip = dataheader)
if (length(nam <- grep("Sentrix_Position", names(df),
ignore.case = TRUE, value = TRUE)) == 1) {
df$Array <- df[, nam]
df[, nam] <- NULL
}
if (length(nam <- grep("Array[\\._]ID", names(df), ignore.case = TRUE,
value = TRUE)) == 1) {
df$Array <- df[, nam]
df[, nam] <- NULL
}
if (!"Array" %in% names(df))
warning(sprintf("Could not infer array name for file: %s",
file))
if (length(nam <- grep("Sentrix_ID", names(df), ignore.case = TRUE,
value = TRUE)) == 1) {
df$Slide <- df[, nam]
df[, nam] <- NULL
}
if (length(nam <- grep("Slide[\\._]ID", names(df), ignore.case = TRUE,
value = TRUE)) == 1) {
df$Slide <- df[, nam]
df[, nam] <- NULL
}
if (!"Slide" %in% names(df))
warning(sprintf("Could not infer slide name for file: %s",
file))
if (length(nam <- grep("Plate[\\._]ID", names(df), ignore.case = TRUE,
value = TRUE)) == 1) {
df$Plate <- df[, nam]
df[, nam] <- NULL
}
if (!is.null(df$Array)) {
patterns <- sprintf("%s_%s_Grn.idat", df$Slide, df$Array)
allfiles <- list.files(dirname(file), recursive = recursive,
full.names = TRUE)
basenames <- sapply(patterns, function(xx) grep(xx,
allfiles, value = TRUE))
names(basenames) <- NULL
basenames <- sub("_Grn\\.idat", "", basenames, ignore.case = TRUE)
df$Basename <- basenames
}
df
}
if (!all(file.exists(base)))
stop("'base' does not exists")
info <- file.info(base)
if (!all(info$isdir) && !all(!info$isdir))
stop("'base needs to be either directories or files")
if (all(info$isdir)) {
csvfiles <- list.files(base, recursive = recursive, pattern = pattern,
ignore.case = ignore.case, full.names = TRUE)
if (verbose) {
cat("Found the following CSV files:\n")
print(csvfiles)
}
}
else csvfiles <- list.files(base, full.names = TRUE)
dfs <- lapply(csvfiles, readSheet)
namesUnion <- Reduce(union, lapply(dfs, names))
df <- do.call(rbind, lapply(dfs, function(df) {
newnames <- setdiff(namesUnion, names(df))
newdf <- matrix(NA, ncol = length(newnames), nrow = nrow(df),
dimnames = list(NULL, newnames))
cbind(df, as.data.frame(newdf))
}))
df
}
read.450k.exp <- function (base, targets = NULL, extended = FALSE, recursive = FALSE,
verbose = FALSE)
{
if (!is.null(targets)) {
if (!"Basename" %in% names(targets))
stop("Need 'Basename' amongst the column names of 'targets'")
files <- targets$Basename
rgSet <- read.450k(files, extended = extended, verbose = verbose)
pD <- targets
pD$filenames <- files
rownames(pD) <- sampleNames(rgSet)
pData(rgSet) <- pD
return(rgSet)
}
Grn.files <- list.files(base, pattern = "_Grn.idat$", recursive = recursive,
ignore.case = TRUE, full.names = TRUE)
Red.files <- list.files(base, pattern = "_Red.idat$", recursive = recursive,
ignore.case = TRUE, full.names = TRUE)
if (length(Grn.files) == 0 || length(Red.files) == 0)
stop("No IDAT files were found")
commonFiles <- intersect(sub("_Grn.idat$", "", Grn.files),
sub("_Red.idat$", "", Red.files))
if (length(commonFiles) == 0)
stop("No IDAT files with both Red and Green channel were found")
commonFiles.Grn <- paste(commonFiles, "_Grn.idat", sep = "")
commonFiles.Red <- paste(commonFiles, "_Red.idat", sep = "")
if (!setequal(commonFiles.Grn, Grn.files))
warning(sprintf("the following files only exists for the green channel: %s",
paste(setdiff(Grn.files, commonFiles.Grn), collapse = ", ")))
if (!setequal(commonFiles.Red, Red.files))
warning(sprintf("the following files only exists for the red channel: %s",
paste(setdiff(Red.files, commonFiles.Red), collapse = ", ")))
rgSet <- read.450k(basenames = commonFiles, extended = extended,
verbose = verbose)
rgSet
}
read.450k <- function (basenames, extended = FALSE, verbose = FALSE)
{
basenames <- sub("_Grn\\.idat$", "", basenames)
basenames <- sub("_Red\\.idat$", "", basenames)
G.files <- paste(basenames, "_Grn.idat", sep = "")
names(G.files) <- basename(basenames)
if (!all(file.exists(G.files))) {
noexits <- G.files[!file.exists(G.files)]
stop("The following specified files do not exist:", paste(noexits,
collapse = ", "))
}
R.files <- paste(basenames, "_Red.idat", sep = "")
names(R.files) <- basename(basenames)
if (!all(file.exists(R.files))) {
noexits <- R.files[!file.exists(G.files)]
stop("The following specified files do not exist:", paste(noexits,
collapse = ", "))
}
stime <- system.time({
G.idats <- lapply(G.files, function(xx) {
if (verbose)
cat("Reading", basename(xx), "\n")
readIDAT(xx)
})
R.idats <- lapply(R.files, function(xx) {
if (verbose)
cat("Reading", basename(xx), "\n")
readIDAT(xx)
})
})[3]
if (verbose)
cat("Read idat files in ", stime, "seconds\n")
if (verbose)
cat("Creating data matrices ... ")
stime <- system.time({
GreenMean <- do.call(cbind, lapply(G.idats, function(xx) xx$Quants[,
"Mean"]))
RedMean <- do.call(cbind, lapply(R.idats, function(xx) xx$Quants[,
"Mean"]))
if (extended) {
GreenSD <- do.call(cbind, lapply(G.idats, function(xx) xx$Quants[,
"SD"]))
RedSD <- do.call(cbind, lapply(R.idats, function(xx) xx$Quants[,
"SD"]))
NBeads <- do.call(cbind, lapply(G.idats, function(xx) xx$Quants[,
"NBeads"]))
}
})[3]
if (verbose)
cat("done in", stime, "seconds\n")
if (verbose)
cat("Instantiating final object ... ")
stime <- system.time({
if (extended) {
out <- new("RGChannelSetExtended", Red = RedMean,
Green = GreenMean, RedSD = RedSD, GreenSD = GreenSD,
NBeads = NBeads)
}
else {
out <- new("RGChannelSet", Red = RedMean, Green = GreenMean)
}
featureNames(out) <- rownames(G.idats[[1]]$Quants)
annotation(out) <- c(array = "IlluminaHumanMethylation450k",
annotation = .default.450k.annotation)
})[3]
if (verbose)
cat("done in", stime, "seconds\n")
out
}