circos_prep: Generate Perl Circos Plot Files

In umccr/rock: Rocking R at UMCCR

Description

Generates required files for a Perl circos plot containing Manta structural variants and/or CNVkit/FACETS/PURPLE/TitanCNA copy number variants.

Usage

circos_prep(outdir = "circos", manta = NULL, cnv = NULL, genome = "hg19", ...)

Arguments

outdir	Directory to write the files to.
manta	Path to Manta VCF file.
cnv	Path to copy number call file.
genome	Genome assembly. "hg19" (default) or "hg38". hg19 gets converted to GRCh37 automatically.
...	Additional arguments for prep_manta_vcf.

Value

Generates the required files for a Perl circos plot with structural variant links and/or copy number variant segments. Returns the paths to these files invisibly.

Examples

## Not run: 
manta <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
cnv <- system.file("extdata", "HCC2218_cnvkit-call.cns", package = "pebbles")
outdir <- "~/Desktop/tmp/circos"

circos_prep(outdir = outdir, manta = manta, cnv = cnv)
circos_prep(outdir = outdir, manta = manta) # no CNVs provided
circos_prep(outdir = outdir, manta = manta, genome = "hg19") # no CNVs provided
circos_prep(outdir = outdir, cnv = cnv) # no SVs provided

## End(Not run)

umccr/rock documentation built on Oct. 11, 2020, 8:10 a.m.