karyotype_chromsCN: Karyotype plotting for each chromosome post...

Description Usage Arguments Details Author(s) See Also

View source: R/karyotype_chromsCN.r

Description

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

Usage

1
karyotype_chromsCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,schr,spos,sval,t,name='',parameters,xlim=c(0,2.5),ylim=0:1,maxCn=8)

Arguments

chr

Chromosomes name of segs object. Final version of segs created from patchwork.Medians_n_AI().

start

Start position of segment.

end

End position of segment.

int

Normalized coverage.

ai

Allelic imbalance.

Cn

Copy number.

mCn

mCn.

mchr

Chromosomes name of kbsegs object. Final version of kbsegs created from patchwork.smoothing().

mpos

Middle position of kbsegs segments.

mval

Ratio between kbsegs coverage and refcoverage.

schr

Chromosome names of alf object. Final version of alf created from patchwork.alleledata().

spos

Positions in alf.

sval

Inverse ratio between allele maximum and allele minimum.

t

A list of approximate copynumber and allelic imbalance positions.

name

Name of sample. patchwork.plot sends it as name of the bamfile.

parameters

The parameters sent to patchwork.copynumbers() to be plotted.

xlim

Default is c(0,2.5). Limit of x axis.

ylim

Default is 0:1. Limit of y axis.

maxCn

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

Details

Walkthrough of the plot:

LEFT
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 RIGHT
Vertical axis: Copynumber
Horizontal axis: Chromosomal coordinate

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

UPPER MIDDLE RIGHT
Vertical axis: Total Intensity
Horizontal axis: Chromosomal coordinate

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

LOWER MIDDLE RIGHT

Cytoband information.

BOTTOM RIGHT
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, [email protected] Sebastian DiLorenzo, [email protected]

See Also

patchwork.copynumbers


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