patchwork.region: Detailed view of a selected regions of the genome.

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

Description

Visualises a selected regions on a selected chromosome for closer inspection. Also shows known genes for selected region.

Usage

patchwork.region(CNfile=NULL,chr,region,hg18=F)

Arguments

CNfile	The <sample>_copnumbers.Rdata file generated from patchwork.plot(). If kept at default, NULL, the current working directory will be searched for it.
chr	Which chromosome you wish to view a region of. ex chr="1"
region	The region in chromosomal coordinates you wish to view. ex region=1000000:6000000
hg18	Gene list for hg19 aligned genome is default. Set hg18=T to use hg18 gene list.

Details

Walkthrough of the plot:

TOP LEFT
Vertical axis: Allelic imbalance
Horizontal axis: Normalized coverage

The selected regions segments in color, plotted agains the whole genome background in grey.

TOP RIGHT - TOP
Vertical axis: Normalized coverage
Horizontal axis: Position (Mb)

Normalized coverage of chromosome with selected region highlighted in a transparent red bar.

TOP RIGHT - MIDDLE
Horizontal axis: Position (Mb)

Cytoband information for chromosome with selected region highlighted in a transparent red bar.

TOP RIGHT - BOTTOM
Vertical axis: Allelic imbalance
Horizontal axis: Position (Mb)

Allelic imbalance of chromosome with selected region highlighted in a transparent red bar.

BOTTOM - TOP
Vertical axis: Normalized coverage
Horizontal axis: Position (Mb)

Normalized coverage of the selected region.

BOTTOM - MIDDLE
Horizontal axis: Position (Mb)

Known gene positions which are in the selected region.

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

Allelic imbalance of the selected region.

Author(s)

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

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