AlleleProfileR.setup: Set the configuration parameters for executing an analysis

Description Usage Arguments Value Author(s)

View source: R/functions_main.R

Description

This function will generate a configuration list based on the provided arguments. This list will have the provide in further analysis steps.

Usage

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AlleleProfileR.setup(samples, genes, index, cutoff = 0.02,
  ignore.snp = F, ignore.single = F, ignore.chimeric = F,
  cut.range = 0, alternate = NULL, cutoff.large = 25,
  chimeric.max.insertion.size = 50, suppress.messages = F)

Arguments

samples

Table with all samples entries, as generated by AlleleProfileR.read.folders.

genes

Path to the .csv file containing all gene entries.

index

Path to the .fa file containing the reference genome.

cutoff

Percent value (0 to 1), representing the treshold read count for a certain allelic variant to be included in further analysis.

ignore.snp

Ignore SNPs? Default is FALSE.

ignore.single

Ingore alleles representing a single read pair? Default is FALSE.

ignore.chimeric

Ignore chimeric reads? Default is FALSE.

cut.range

Range around cut site for considering NHEJ. Default is 0, this setting will disregard cut range.

alternate

List of alternate objects for all samples (in order), NULL if not used.

cutoff.large

Cutoff value for determining whether an indel is large or small. Default is 25.

chimeric.max.insertion.size

Max insertion size when inspecting chemeric alignments. Default is 50.

suppress.messages

Suppress messages? Default is FALSE.

Value

list

Author(s)

Arne Bruyneel


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