call_variants: Call Variants

In andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Description

Call all variants from the varscan pileup2cns output given a specific trinucleotide context and the corresponding error model.

Usage

call_variants(i, data, flanking_seqs, error_models)

Arguments

i	Index of the FlankingSeqGroup for which the model is being generated
data	Data.Frame from generate_all_models with FlankingSeqGroup and three empty columns for parameters of model fit
flanking_seqs	String with one of 192 trinucleotide contexts in which variants may be found
error_models	Data.Frame of context specific error models generated from generate_all_models

Value

This function returns a VRanges with the following metadata:

• FlankingSeqGroup

• Model Used

• Model pvalue

andygxzeng/ECSI documentation built on Feb. 6, 2021, 8:53 a.m.