fread.first {PeakSegDisk} | R Documentation |
Read the first line of a text file. Useful for quickly checking if
the coverage.bedGraph_penalty=VALUE_segments.bed file is
consistent with the coverage.bedGraph_penalty=VALUE_loss.tsv
file. (used by the PeakSegFPOP_dir
caching mechanism)
fread.first(file.name, col.name.vec)
file.name |
Name of file to read. |
col.name.vec |
Character vector of column names. |
Data table with one row.
Toby Dylan Hocking
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) pstr <- "10.5" PeakSegFPOP_file(tmp, pstr) outf <- function(suffix){ paste0(tmp, "_penalty=", pstr, "_", suffix) } segments.bed <- outf("segments.bed") first.seg.line <- fread.first(segments.bed, col.name.list$segments) last.seg.line <- fread.last(segments.bed, col.name.list$segments) loss.tsv <- outf("loss.tsv") loss.row <- fread.first(loss.tsv, col.name.list$loss) seg.bases <- first.seg.line$chromEnd - last.seg.line$chromStart loss.row$bases == seg.bases