pairUpAlignments: Pair up alignments in a GRanges object

Description Usage Arguments Value See Also Examples

View source: R/hiReadsProcessor.R

Description

Given a GRanges object, the function uses specified gaplength parameter to pair up reads where the qName column ends with "atpersand pairname atpersand" which is outputted by extractSeqs.

Usage

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pairUpAlignments(psl.rd = NULL, maxGapLength = 2500, sameStrand = TRUE,
  parallel = TRUE)

Arguments

psl.rd

a GRanges object with qNames ending in "atpersand pairname atpersand".

maxGapLength

maximum gap allowed between end of pair1 and start of pair2. Default is 2500 bp.

sameStrand

should pairs be aligned to the same strand or in same orientationin the reference genome? Default is TRUE. This is 'TRUE' because pair2 reads are reverseComplemented when reading in data in findBarcodes

parallel

use parallel backend to perform calculation with BiocParallel. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using SerialParam.

Value

a GRanges object with reads paired up denoted by "paired" column. Improper pairs or unpaired reads are returned with "paired" column as FALSE.

See Also

pairwiseAlignSeqs, blatSeqs, read.blast8, read.psl, getIntegrationSites, read.BAMasPSL

Examples

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psl.rd <- read.BAMasPSL(bamFile=c("sample1hits.bam","sample2hits.bam"))
pairUpAlignments(psl.rd)

malnirav/hiReadsProcessor documentation built on Sept. 17, 2017, 10:56 a.m.