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

Description Usage Arguments Value Author(s) Examples

Description

Import a psl formatted alignment file of queries to targets

Usage

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  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

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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.