hrdetect_prep_sv: Prepare VCF with SVs for use with HRDetect

Description Usage Arguments Value Examples

View source: R/hrdetect.R

Description

Prepares VCF with SVs for use with HRDetect.

Usage

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hrdetect_prep_sv(x, nm = NULL, genome = "hg38")

Arguments

x

Path to VCF with SVs.

nm

Sample name.

genome

Human genome version (default: hg38. hg19 means GRCh37).

Value

Single-column data.frame (with rownames) with counts for each SV category.

Examples

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x <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
nm <- "SampleA"
(d <- hrdetect_prep_sv(x, nm))

umccr/gpgr documentation built on Nov. 25, 2021, 1:15 p.m.