CG_karyotype: CompleteGenomics karyotype plotting function

Description Usage Arguments Details Author(s) See Also

Description

Plots each, color coded by chromosomal coordinate, chromosome against a background of the complete genome.

Usage

1

Arguments

chr

Chromosomes name of segm object, as generated from somaticCnvSegmentsNonDiplod file.

start

Start position of segment.

end

End position of segment.

int

Ratio between relative coverage and segment length.

ai

Allelic imbalance.

name

Default is ”. Plot generated as "name_karyotype.png" in your working directory.

xlim

Default is c(0,2.4). Limit of x axis.

ylim

Default is c(0,1). Limit of y axis.

Details

Vertical axis: Allelic imbalance.
Horizontal axis: Total intensity.

The plot is a overview, for a closer look see the plots generated by CG_KaCh().

Author(s)

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

See Also

patchwork.CG.plot
CG_KaCh


patchworkCG documentation built on May 2, 2019, 6:47 p.m.