import.psl: Import a psl formatted alignment file of queries to targets

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

Description

Import a psl formatted alignment file of queries to targets

Usage

  import.psl(x, score = TRUE, target2chromosome = FALSE)

Arguments

x	the filename of a psl alignment, with or without a pslHeader.
score	logical: if TRUE, calculate the alignment score for all genomic alignments
target2chromosome	If psl contains alignments to a chromosome, then you can convert the FastA header chromosome name to the human readable form of “chr11” for example.

Value

a data.frame representation of a psl file

Author(s)

Mark Cowley, 12 April 2006

Examples

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

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

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