hiReadsProcessor (version 1.8.2)

pslToRangedObject: Convert psl dataframe to GRanges

Description

Convert psl dataframe to GRanges object using either the query or target as the reference data column.

Usage

pslToRangedObject(x, useTargetAsRef = TRUE, isblast8 = FALSE)

Arguments

x

dataframe reflecting psl format

useTargetAsRef

use target(tName) or query(qName) as the chromosome or the reference data. Default is TRUE.

isblast8

the input dataframe blast8 format output from BLAT. Default is FALSE.

Value

• a GRanges object reflecting psl file type.

See Also

read.psl, read.blast8, blatListedSet

Examples

data(psl)
psl <- head(psl)
pslToRangedObject(psl)
pslToRangedObject(psl, useTargetAsRef=FALSE)