karyotype_check: Karyotype check function

In patchwork: Allele-specific Copy Number Analysis of whole genome data

Description

Plots the whole genome coverage vs allelic imbalance with the approximated areas copynumbers and allele constitution. Karyotype_check is called from patchwork.copynumbers function.

Usage

karyotype_check(chr,start,end,int,ai,Cn,mCn,t,name='',xlim=c(-1.02,1.02),ylim=0:1)

Arguments

chr	Chromosome.
start	Start position of segment.
end	End position of segment.
int	Mean.
ai	Allelic imbalance.
Cn	Copy number.
mCn	Minor Copy Number
t	A list between int and ai.
name	Default is BamFile argument from patchwork.plot is used as argument.
xlim	Default is c(-1.02,1.02). Limit of x axis.
ylim	Default is 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 alleles 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.

Run within patchwork.copynumbers function. copynumbers.Rdata must be in working directory for that function to run, and thus this one aswell as most of its input is taken from segs.

Author(s)

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

See Also

patchwork.copynumbers

patchwork documentation built on May 2, 2019, 5:02 p.m.