col.name.list: col name list

Description Usage Examples

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

1
"col.name.list"

Examples

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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)

PeakSegDisk documentation built on Sept. 11, 2019, 9:07 a.m.