downloadBigWigs: downloadBigWigs

In tdhock/PeakSegPipeline: Genome-Wide Peak Prediction Using Supervised Learning and Optimal Segmentation

Description

Download bigWig files from a trackDb file.

Usage

downloadBigWigs(trackDb.txt, 
    out.dir, verbose = getOption("PeakSegPipeline.verbose", 
        1))

Arguments

trackDb.txt	trackDb text file.
out.dir	Output directory.
verbose	Print messages?

Value

Nothing.

Author(s)

Toby Dylan Hocking

Examples

## Create a trackDb.txt file with links to a few small bigWig files on GitHub.
bigWig.part.vec <- c(
  "Input/MS010302",
  "bcell/MS010302",
  "Input/MS002201",
  "kidney/MS002201")
repos.url <- "https://raw.githubusercontent.com/tdhock/input-test-data/master/"
track.lines <- sprintf(
  "track %s\nbigDataUrl %s%s.bigwig\n",
  sub("/", "_", bigWig.part.vec),
  repos.url, bigWig.part.vec)
track.dir <- tempfile()
dir.create(track.dir)
trackDb.txt <- file.path(track.dir, "trackDb.txt")
cat(track.lines, sep="\n")
writeLines(track.lines, trackDb.txt)

## Download the bigWig files mentioned in trackDb.txt
if(interactive()){
  downloadBigWigs(trackDb.txt, track.dir, verbose=1)
}

tdhock/PeakSegPipeline documentation built on March 3, 2020, 1:35 a.m.