load_as_VRanges: Load as VRanges

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

Description

Load varscan pileup2cns output from a given sample as a VRanges object

Usage

load_as_VRanges(sample_name, sample_path, genome, metadata = TRUE)

Arguments

sample_name	Name of the sample
sample_path	Sample file location
genome	Reference genome to use.
metadata	Logical. Whether to include metadata (VAF, quality scores, strand-specific counts)

Value

This function returns a VRanges object with the following information:

• seqnames

• ranges

• ref

• alt

• refdepth

• altdepth

• sampleNames

• metadata (optional)

Examples

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

## End(Not run)

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