karyotype_chroms: Karyotype plotting of each chromosome
In patchwork: Allele-specific Copy Number Analysis of whole genome data

Description Usage Arguments Details Author(s) See Also

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

1	karyotype_chroms(chr,start,end,int,ai,mchr,mpos,mval,schr,spos,sval,name='',xlim=c(0,2.5),ylim=0:1,MAPD=" ",MHOF=" ")

`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.
`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.
`name`	Name of sample. patchwork.plot sends it as name of the bamfile.
`xlim`	Default is c(0,2.5). Limit of x axis.
`ylim`	Default is 0:1. Limit of y axis.
`MAPD`	Placeholder for later sample measures.
`MHOF`	Placeholder for later sample measures.

Walkthrough of the plot:

TOP
Vertical axis: Allelic Imbalance
Horizontal axis: Normalized coverage

The chromosome plotted against the complete genome background. The separation between clusters within the plot are due to the fluctuating coverage 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.

MIDDLE
Vertical axis: Normalized coverage
Horizontal axis: Position (Mb)

The chromosome in questions normalized coverage plotted against the position on the chromosome.

CYTOBAND

Cytoband information for selected chromosome.

BOTTOM
Vertical axis: Allelic imbalance
Horizontal axis: Position (Mb)

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

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

patchwork.plot
karyotype

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