col.name.list | R Documentation |
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
.
"col.name.list"
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)