plotCoverage: Plot coverage of 450K across hg19
In sean-cho/Epicopy: Get CNV information from 450K array

Description Usage Arguments Details Value Examples

View source: R/plotCoverage.R

Plots the coverage of 450K array probes of specified chromosome range in specified window sizes.

1	plotCoverage(chr, winSize = 1e+06, maxVal = 50, chrRange = NULL, ...)

`chr`	Chromosome to plot.
`winSize`	Window size of segments.
`maxVal`	Upper limit of number of probes for darkest color.
`chrRange`	Region (in bases) of the chromosome to plot. If NULL plots the whole chromosome.

plotCoverage Plots the coverage of 450K array across the genome.

Uses hg19 annotations. winSize specifies window sizes and maxVal controls the number of probes for the darkest color in the window.

A plot of 450K coverage in user defined windows.

# Plot coverage through the whole of chromosome two
plotCoverage('chr2')

# Plot coverage through the whole of chromosome two with windows of 2Mb and max of 200 probes
plotCoverage('chr2', winSize = 2e6, maxVal = 200)