viewGenome-package: View human genome in cytobands

In Yves-CHEN/viewGenome: This is a collection of plots designed to view human genome by per chromosomes with cytobands, or view in d.SKY

Description

This is designed to view human genome with a chromsomal ideogram (HG19). The plot function has a "chr" parameter, which specify the specific chromosome to plot.
e.g. https://www.pinterest.com/pin/475411304393375351/
The plots includes

• the regular 2D plot with a cytoband in the x-axis,

• A digital SKY-Plot. This provides a view of the genome, with copy number alterations.

Usage

## Default S3 method:
 myplot(x,y, chr, chrWidth = 0.3, col = 1, graybg = F, checks = c(1,10000000),...)
## Default S3 method:
 plotPloidy(chr, CN, col=2, lwd=0.4, chrWidth=0.6, maxCN=12, ...)
## Default S3 method:
 genomeInSubplots(x, y, grouping)

Arguments

x	A numeric vector for the location.
y	A numeric vector for copy numbers (or other informations, e.g. depth).
chrWidth	Indicate the width of the cytobands plotted at bottom.
col	A single numeric number of color code.
...	These parameters will be passed to plot function.
CN	CN is a data.frame, with 4 colums of startPos, endPos, copy number, minor allele copy number.
grouping	grouping should have length as x. It specifies which of the x belonging to which group.
pch	specify the shape of the brush for painting.
type	type of the dots. e.g. "l" for line, "p" for point. see par

Author(s)

Wenhan Chen

Examples

    library(viewGenome)
    runtest()

Yves-CHEN/viewGenome documentation built on May 10, 2019, 1:54 a.m.