CG_Ka_check: Karyotype check function

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

Description

Plots the whole genome coverage vs allelic imbalance with the approximated areas copynumbers and allele constitution. CG_Ka_check is called from the patchwork.CG.copynumbers() function. It would be hard to run this function outside of patchwork.CG.copynumbers().

Usage

CG_Ka_check(chr,start,end,int,ai,Cn,mCn,t,name='',xlim=c(0,2.4),ylim=c(0,1))

Arguments

chr	Chromosome.
start	Start position of segment.
end	End position of segment.
int	Ratio between relative coverage and segment length.
ai	Allelic imbalance as calculated from (1 - (lesser readcount / greater readcount)) per segment.
Cn	Copy number object created in patchwork.CG.copynumbers().
mCn	mCn, object created in patchwork.CG.copynumbers().
t	A list between int and ai. (ratio and allelic imbalance)
name	Default is ”. When method is run by patchwork.CG.copynumbers() it will inherit that functions name parameter.
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: Relative coverage.

The naming scheme is Copynumber-m-LesserAlleleDistribution So for example 2m0 means copynumber = 2, both allels are the same whereas 2m1 means copynumber = 2, 1 allele each.

Another example: 4m0, copynumber = 4, All allels are the same. (Loss of heterozygosity). 4m1, copynumber = 4, 3 alleles are the same, one is different. 4m2, copynumber = 4, 2 alleles each.

The total number of alleles present are always the copynumber.

Author(s)

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

See Also

patchwork.CG.copynumbers

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