col.name.list {PeakSegDisk} | R Documentation |
col name list
Description
Named list of character vectors (column names of bed/bedGraph/tsv
files), used to read data files, which do not contain a header /
column names. Each name corresponds to a data/file type, and each
value is a character vector of column names expected in that
file. loss is for the coverage.bedGraph_penalty=VALUE_loss.tsv
file generated by PeakSegFPOP_file
; segments is for the
coverage.bedGraph_penalty=VALUE_segments.bed generated by
PeakSegFPOP_file
; coverage is for the coverage.bedGraph file which
is used as input to PeakSegFPOP_file
.
Usage
"col.name.list"
Examples
library(PeakSegDisk)
r <- function(chrom, chromStart, chromEnd, coverage){
data.frame(chrom, chromStart, chromEnd, coverage)
}
four <- rbind(
r("chr1", 0, 10, 2),
r("chr1", 10, 20, 10),
r("chr1", 20, 30, 14),
r("chr1", 30, 40, 13))
write.table(
four, tmp <- tempfile(),
sep="\t", row.names=FALSE, col.names=FALSE)
read.table(
tmp, col.names=col.name.list$coverage)
pstr <- "10.5"
PeakSegFPOP_file(tmp, pstr)
outf <- function(suffix){
paste0(tmp, "_penalty=", pstr, "_", suffix)
}
fread.first(outf("segments.bed"), col.name.list$segments)
fread.first(outf("loss.tsv"), col.name.list$loss)
[Package PeakSegDisk version 2023.11.27 Index]