plotHMMscore: Plot CNV inference score.

In zhouzilu/iCNV: Integrated Copy Number Variation detection

Description

Plot out CNV inference score. Each row is a sample, each column is a SNP or, exon (WES) or bin (WGS). Red color indicate score favor duplication whereas blue favor deletion.

Usage

plotHMMscore(icnv_res, h = NULL, t = NULL, title = "score plot",
  output = NULL, col = "")

Arguments

icnv_res	CNV inference result. Result from iCNV_detection() (i.e. iCNV_detection(...))
h	start position of this plot. Default Start of the whole chromosome
t	end position of this plot. Default End of the whole chromosome
title	of this plot. Character value. Type character Default "score plot"
output	generated from output_list_function. If it isn't null, only CNVs in output file will be highlighted. Default NULL
col	Specify if would like to plot in DGV color scheme ('DGV',red for deletion, blue for duplication and grey for diploid) or default color scheme (blue for deletion, red for duplicatin and and green for diploid) Type character. Default ”

Value

void

Examples

plotHMMscore(icnv_res0,h=21000000, t=22000000, title='my favorite subject')
plotHMMscore(icnv_res0,h=21000000, t=22000000, title='my favorite subject',col='DGV')

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