AlleleProfileR.binreads: Bin reads based on genomic postition with respect to certain...

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

This function will assign the reads within a certain PCR pre-amplification region to different bins, depending on whether they do/do not/or partly overlap with the ROI. A read will be classified as 'A' if it is within the PCR amplification range (pcrrange). A read will be classified as 'B' or 'C' if it lies upstream and partly overlaps OR lies downstream and partly overlaps with the region of interest (range). Finally, a read will be flagged as 'D' if it fully overlaps with the ROI.

Usage

AlleleProfileR.binreads(bamtable, chr, pcrrange, range, purify = T)

Arguments

bamtable	Data.frame containing the reads, as generated by AlleleProfileR.bam.
chr	Chromosome
pcrrange	Genomic range of that was pre-amplified by PCR before sequencing.
range	Genomic range of interest, where variants will be called.
purify	If set to TRUE, low qual reads will be discarded. Can be executed separately by AlleleProfileR.qc.simple.

Value

Bam data.frame with added columns 'bin', 'select', 'lower', and 'upper'.

Author(s)

Arne Bruyneel

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.