AlleleProfileR.execute: Wrapper execute function for the analysis

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

Description

This is a background function that will process a single sample for a single gene region.

Usage

AlleleProfileR.execute(bamtable, samplestable, genestable, i, j, cutoff,
  index, ignore.snp, ignore.single, summarize = TRUE, cut.range,
  cutoff.large, ignore.chimeric, chimeric.max.insertion.size,
  suppress.messages = F)

Arguments

bamtable	Data.frame containing the reads, as generated by AlleleProfileR.bam.
samplestable	Samples table, inherited from config.
genestable	Genes table, inherited from config.
i	sample id
j	gene id
cutoff	Percent value (0 to 1), representing the treshold read count for a certain allelic variant to be included in further analysis.
index	Path to the .fa file containing the reference genome.
ignore.snp	Ignore SNPs? Default is FALSE.
ignore.single	Ingore alleles representing a single read pair? Default is FALSE.
summarize	Generate ummary tables and exported as .csv files. Default is TRUE.
cut.range	Range around cut site for considering NHEJ. Default is 0, this setting will disregard cut range.
cutoff.large	Cutoff value for determining whether an indel is large or small. Default is 25.
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.

Author(s)

Arne Bruyneel

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