fread.first: Quickly read first line

In PeakSegDisk: Disk-Based Constrained Change-Point Detection

Quickly read first line

Description

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)

Usage

fread.first(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

PeakSegDisk documentation built on Sept. 8, 2023, 5:50 p.m.