karyotype_chromsCN: Karyotype plotting for each chromosome post...

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

Description

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

Usage

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

See Also

patchwork.copynumbers

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