Nothing
write.bedGraph <- function (x, raw = TRUE, vals = TRUE, directory = ".")
{
for (i in 1:ncol(x)) {
if (class(x) == "ACMECalcSet") {
if (vals) {
filename <- file.path(directory, sprintf("%s_thresh%3.2f.bed",
sampleNames(x)[i], threshold(x)))
cat(filename, "\n")
f = file(filename,'w')
writeLines(sprintf('track type=bedGraph name=%s description=%s',
basename(filename),basename(filename)),con=f)
write.table(data.frame(chromosome = chromosome(x),
start = start(x), end = end(x),
-log10(vals(x)[, i] + min(vals(x)[vals(x)[,i] > 0, i]))),
file = f, sep = "\t",
col.names = FALSE, row.names = FALSE, quote = FALSE)
close(f)
}
}
if (raw) {
filename <- file.path(directory, sprintf("%s_raw.bed",
sampleNames(x)[i]))
cat(filename, "\n")
f = file(filename,'w')
writeLines(sprintf('track type=bedGraph name=%s description=%s',
filename,filename),con=f)
write.table(data.frame(chromosome = chromosome(x),
start = start(x), end=end(x),
exprs(x)[, i]),
file = f,
sep = "\t", col.names = FALSE, row.names = FALSE,
quote = FALSE)
close(f)
}
}
}
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