write.ucsc.track: Write a psl object to a UCSC-style track

In drmjc/blat: Import/Export functions for UCSC genome BLAT alignments

Description

Write a psl object to a UCSC-style track

Usage

  write.psl.track(..., header = FALSE)

  write.bed.track(..., header = TRUE)

  write.ucsc.track(psl, file, name = "localBLAT",
    description = "local BLAT alignment", splitchr = FALSE,
    pack.tracks = c("knownGene", "mgcGenes", "mrna", "multiz17way"),
    dense.tracks = c("ruler", "refGene", "xenoRefGene", "ensGene", "intronEst", "snp126", "rmsk", "cytoBand", "stsMapMouseNew", "miRNA"),
    colour = c(0, 0, 0), useScore = FALSE, method = "psl",
    header = TRUE)

Arguments

...	arguments passed to write.ucsc.track
psl	a PSL object
file	the output file name
name	the track name
description	the track description
splitchr	logical. default=FALSE
pack.tracks	character vector of UCSC track names to be displaed in 'pack' form
dense.tracks	character vector of UCSC track names to be displaed in 'dense' form
colour	numeric vector[3]
useScore	logical
method	one of “psl”, “bed”,
header	logical. default=TRUE

Value

nothing. writes files.

Author(s)

Mark Cowley, 2013-05-30

Examples

f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)
out <- tempfile(fileext=".psl")
write.psl.track(psl, file=out)
cat("wrote to: ", out, "\n")
f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)
out <- tempfile(fileext=".bed")
write.bed.track(psl, file=out)
cat("wrote to: ", out, "\n")
f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)

out <- tempfile(fileext=".psl")
write.ucsc.track(psl, file=out, method="psl")
cat("wrote to: ", out, "\n")

out <- tempfile(fileext=".bed")
write.ucsc.track(psl, file=out, method="bed")
cat("wrote to: ", out, "\n")

drmjc/blat documentation built on May 15, 2019, 2:22 p.m.