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

Description Usage Arguments Value Examples

View source: R/icnv_output_to_gb.R

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

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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

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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)

iCNV documentation built on Nov. 8, 2020, 11:12 p.m.