starfish_link: starfish_link

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

starfish_link

Description

This function loads a SV dataframe and generates "seed" CGR regions, "connected" CGR regions, and complex SVs.

Usage

starfish_link(sv_file, prefix = "")

Arguments

sv_file	a SV dataframe with 8 columns: "chrom1","pos1", "chrom2","pos2","svtype" (DEL,DUP,h2hINV,t2tINV,TRA),"strand1" (+/-) and "strand2" (+/-),"sample". Other svtypes like INV, INS, BND are not accepted
prefix	the prefix for all intermediate files, default is none

Value

a list of files: $interleave_tra_complex_sv contains complex SVs, $mergecall contains "seed" CGR regions, and $starfish_call contains "connected" CGR regions.

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