sequence_context: Sequence Context

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

Description

Get sequence context for a VRanges object of the varscan pileup2cns output

Usage

sequence_context(sample, genome, context = 3)

Arguments

sample	VRanges object of the varscan pileup2cns output
genome	Genome of input object, either hg19 or hg38
context	Number of nucleotides to return. For example, 3 would return three nucleotides with the position of the variant being the middle nucleotide.

Value

This function returns the VRanges object with the additional metadata column context.

Examples

## Not run: 
variants <- load_as_VRanges(sample_name = "pt123",
    sample_path = "./patient_123_pileup2cns", genome = "hg19", metadata = TRUE)
variants <- sequence_context(sample = variants, context = 3)

## End(Not run)

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