pslToRangedObject: Convert psl dataframe to GRanges

In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

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)

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.