Karyotype plotting for each chromosome post patchwork.CG.copynumbers().

Description

Visualizes the calculated data of patchwork.CG.plot() + patchwork.CG.copynumbers() for each chromosome. See details for a walkthrough of the plot.

Usage

1
CG_KaChCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,sval,schr,spos,name='',xlim=c(0,2.4),ylim=c(0,1),maxCn=8)

Arguments

chr

Chromosomes name of segm object.

start

Start position of segment.

end

End position of segment.

int

Ratio of relative coverage from somaticCnvSegmentsNonDiplod file and segment length.

ai

Allelic imbalance.

Cn

Copy number.

mCn

mCn.

mchr

Chromosomes name of depcov (depthOfCoverage file).

mpos

Start position from depcov.

mval

Ratio between averagenormalizedcoverage and mean(averagenormalizedcoverage) from depthOfCoverage file.

sval

Inverse ratio between allele maximum and allele minimum per position.

schr

Chromosomes name of mastervar.

spos

Start position from mastervar.

name

Name that you want output to have. Default is ” which will yield files named as '_KaChCN_chr#.png'. When method is run by patchwork.CG.copynumbers() it will 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.

maxCn

Default is 8. The highest copynumber of the sample to check for.

Details

Walkthrough of the plot:

TOP
Vertical axis: Allelic Imbalance
Horizontal axis: Total Intensity

The chromosome plotted against the complete genome background. The separation between clusters within the plot are due to the fluctuating intensity and allelic imbalance and as such display the varying allele counts and copy numbers. Longer/larger segments have bigger circles. Darker circles show more content as they are ontop of eachother.

TOP MIDDLE
Vertical axis: Copynumber
Horizontal axis: Chromosomal coordinate

Displays the total and minor copynumbers for different segments of the chromosome in question.

LOWER MIDDLE
Vertical axis: Total Intensity
Horizontal axis: Chromosomal coordinate

The chromosome in questions total intensity plotted against the position on the chromosome.

BOTTOM
Vertical axis: Allelic Imbalance
Horizontal axis: Chromosomal coordinate

The chromosome in questions allelic imbalance plotted against the position on the chromosome.

Author(s)

Markus Mayrhofer, markus.mayrhofer@medsci.uu.se Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se

See Also

patchwork.CG.copynumbers