write.psl: Write a psl object out to a psl file.

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

Description

Useful if you want to use the kent utilities on the psl object that you've been modifying in R. Note this ignores the psl$score, as per the PSL file format.

Usage

  write.psl(psl, out, header = TRUE)

Arguments

psl	a psl data.frame from import.psl or new.psl (with or without score column)
out	the outfilename or con (see write, write.delim)
header	logical: write the psl header?

Author(s)

Mark Cowley, 13 March 2007

Examples

f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=TRUE)

out <- tempfile(fileext=".psl")
write.psl(psl, out, header=FALSE)
cat("wrote to: ", out, "\n")

out <- tempfile(fileext=".psl")
write.psl(psl, out, header=TRUE)
cat("wrote to: ", out, "\n")

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