fread.last {PeakSegDisk}

Quickly read last line

Description

Read the last 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)

Usage

fread.last(file.name, 
    col.name.vec)

Arguments

file.name

Name of file to read.

col.name.vec

Character vector of column names.

Value

Data table with one row.

Author(s)

Toby Dylan Hocking

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)
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