psl2bed: Convert a psl alignment from BLAT into a BED alignment.

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

Description

Convert a psl alignment from BLAT into a BED alignment.

Usage

  psl2bed(psl, col = "0,0,0", calc.score = FALSE)

Arguments

psl	A psl alignment object
col	the colour, in the form of a character vector. default: “0,0,0”
calc.score	logical. if TRUE, then the BED score (column 5) will be calculated. see pslScore. if FALSE, then the Score (column 5) will be the psl$score, if present or 1000.

Value

a BED-formatted data.frame.

TODO

thickStart and thickEnd are currently just the same as "T start" and "T end"

Author(s)

Mark Cowley, 5 Jan 2007

Examples

f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)
head(psl2bed(psl))
head(psl2bed(psl, calc.score=T))

psl <- import.psl(f, score=TRUE)
head(psl2bed(psl))
head(psl2bed(psl, calc.score=T))

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