karyotype_check: Karyotype check function

Description Usage Arguments Details Author(s) See Also

View source: R/karyotype_check.r

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

1
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, [email protected] Sebastian DiLorenzo, [email protected]

See Also

patchwork.copynumbers


xu-chang/patchwork-lite documentation built on March 19, 2018, 3:09 a.m.