Description Usage Arguments Value Author(s) Examples
Write a psl object to a UCSC-style track
1 2 3 4 5 6 7 8 9 10 | 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 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= |
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= |
nothing. writes files.
Mark Cowley, 2013-05-30
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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")
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