icnv_output_to_gb: Convert icnv.output to input for Genome Browser.

In zhouzilu/iCNV: Integrated Copy Number Variation detection

Description

We could add the output to custom tracks on Genome Browser. Remeber to choose human assembly matches your input data. We color coded the CNVs to make it as consistant as IGV. To show color, click 'User Track after submission', and edit config to 'visibility=2 itemRgb="On"'. Color see Github page for more example.

Usage

icnv_output_to_gb(chr = numeric(), icnv.output)

Arguments

chr	CNV chromosome. Type integer.
icnv.output	output from output_list_function

Value

matrix for Genome browser

Examples

icnv.output <- output_list(icnv_res=icnv_res0,sampleid=sampname_qc, CN=0, min_size=10000)
gb_input <- icnv_output_to_gb(chr=22,icnv.output)
write.table(gb_input,file='icnv_res_gb_chr22.tab',quote=FALSE,col.names=FALSE,row.names=FALSE)

zhouzilu/iCNV documentation built on Feb. 16, 2020, 4:53 p.m.