starfish_plot: starfish_plot

In yanglab-computationalgenomics/Starfish: Detecting connected CGR regions and inferring mechanisms from structural variation and copy number data

starfish_plot

Description

This function loads a SV dataframe, a CNV dataframe and "connected" CGR regions reported by starfish_link, to draw the connected regions in a linear setting.

Usage

starfish_plot(sv_file, cnv_file, cgr, genome_v = "hg19")

Arguments

sv_file	a SV dataframe with "chrom1","end1", "chrom2","end2","svtype","strand1","strand2","sample"
cnv_file	a CNV dataframe with "chromosome","start","end","total_cn","sample"
cgr	"connected" CGR regions, output from starfish_link
genome_v	genome version of "hg19" or "hg38", default is "hg19"

Value

plots of "connected" CGR regions.

yanglab-computationalgenomics/Starfish documentation built on July 27, 2022, 10:26 a.m.