CG_karyotype: CompleteGenomics karyotype plotting function

In patchworkCG: Allele-specific Copy Number Analysis of CompleteGenomics Whole Genome data

Description

Plots each, color coded by chromosomal coordinate, chromosome against a background of the complete genome.

Usage

CG_karyotype(chr,start,end,int,ai,name,xlim,ylim)

Arguments

chr	Chromosomes name of segm object, as generated from somaticCnvSegmentsNonDiplod file.
start	Start position of segment.
end	End position of segment.
int	Ratio between relative coverage and segment length.
ai	Allelic imbalance.
name	Default is ”. Plot generated as "name_karyotype.png" in your working directory.
xlim	Default is c(0,2.4). Limit of x axis.
ylim	Default is c(0,1). Limit of y axis.

Details

Vertical axis: Allelic imbalance.
Horizontal axis: Total intensity.

The plot is a overview, for a closer look see the plots generated by CG_KaCh().

Author(s)

Markus Mayrhofer, [e-mail]
Sebastian DiLorenzo, [e-mail]

See Also

patchwork.CG.plot
CG_KaCh

patchworkCG documentation built on May 2, 2019, 6:47 p.m.