plotSnp {SNPchip}R Documentation

Plots copy number and genotype calls against physical position

Description

Returns an object inheriting from class ParESet – essentially, a list of default graphical parameters that can be modified as needed. The show method for this class plots the copy number and genotype calls versus physical position for an arbitrary number of samples and chromosomes.

Usage

plotSnp(object, hmmPredict, ...)
## S4 method for signature 'SnpLevelSet':
plot(x, y, ...)

Arguments

object, x An object extending ParESet
hmmPredict, y An object of class HmmPredict
... Additional arguments to the initialization methods of the ParESet classes

Details

See examples in the vignette

Author(s)

R. Scharpf

See Also

par, ParESet-class, ParSnpCallSet-class, ParSnpCopyNumberSet-class, ParSnpSet-class

Examples

data(sample.snpset)
chr1 <- sample.snpset[chromosome(sample.snpset) == "1", 1]
graph.par <- plotSnp(chr1)
class(graph.par)
## Not run: 
graph.par
## End(Not run)

[Package SNPchip version 1.6.0 Index]