AlleleProfileR.determine.variants: Determine the allelic variants for a sample and gene

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

Description

This is the main worker function that parses through the reads in the bam file and determines their allele variants.

Usage

AlleleProfileR.determine.variants(bamtable, index, gene,
  cutoff.large = 25, ignore.snp = F, cut.range = 0,
  ignore.chimeric = F, chimeric.max.insertion.size = 50,
  suppress.messages = F)

Arguments

bamtable	Data.frame containing the reads, as generated by AlleleProfileR.bam.
index	Path to the .fa file containing the reference genome.
gene	Gene information vector
cutoff.large	Cutoff value for determining whether an indel is large or small. Default is 25.
ignore.snp	Ignore SNPs? Default is FALSE.
cut.range	Range around cut site for considering NHEJ. Default is 0, this setting will disregard cut range.
ignore.chimeric	Ignore chimeric reads? Default is FALSE.
chimeric.max.insertion.size	Max insertion size when inspecting chemeric alignments. Default is 50.
suppress.messages	Suppress messages? Default is FALSE.

Value

Variants data.frame

Author(s)

Arne Bruyneel

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