viewGenome-package: View human genome in cytobands

Description Usage Arguments Author(s) Examples

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

Usage

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## 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

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Yves-CHEN/viewGenome documentation built on Aug. 3, 2017, 3:42 a.m.