readPsl: readPsl

In NBISweden/genecovr: Gene body coverage analysis to evaluate genome assemblies

readPsl

Description

Read psl output

Usage

readPsl(
  filename,
  seqinfo.query = NULL,
  seqinfo.sbjct = NULL,
  metadata = list(),
  ...
)

Arguments

filename	input filename
seqinfo.query	Seqinfo object for query (transcripts)
seqinfo.sbjct	Seqinfo object for subject (reference)
metadata	metadata for AlignmentPairs result
...	additional parameters

Details

Parse Pattern Space Layout (psl) file; see http://genome.ucsc.edu/FAQ/FAQformat.html for more information on the psl file format

Value

AlignmentPairs object

Examples

fn <- system.file("extdata", "transcripts2polished.psl",
      package="genecovr")
ap <- readPsl(fn)

NBISweden/genecovr documentation built on Jan. 26, 2024, 7:15 a.m.