plotSNPs: Make M vs S plot for SNPs or samples.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plot.R

Description

These functions plot the M-values (log-ratios) versus S-values (average intensities) for given SNP/(s) or sample/(s) or beanplots for M-values from different samples.

Usage

1
2
	plotSNPs(cnSet, row=1, offset=0, xlim=c(9,16), ylim=c(-5,5), verbose=FALSE)
	plotSamples(cnSet, col=1, offset=0, xlim=c(9,16), ylim=c(-5,5), verbose=FALSE, sample=100000, seed=1, type="smoothScatter")

Arguments

cnSet

An object of class CNSet

row

scalar/vector of SNP indexes to plot

col

scalar/vector of sample indexes to plot

offset

numeric, offset to add to intensities in cnSet before log2-transforming to make log-ratios or average log-intensities

xlim

the x limits of the plot

ylim

the y limits of the plot

verbose

'logical.' Whether to print descriptive messages during processing

sample

integer indicating the number of SNPs to sample for the plot

seed

integer seed for the random number generator to sample the SNPs

type

character vector specifying the type of sample plot (either 'smoothScatter' or 'beanplot')

Details

The plotSNPs and plotSamples functions plot the M and S values derived from the cnSet object.

Value

One or more M vs S plot for plotSNPs for a given SNP(/s) or either a smoothed scatter plot of M vs S or a beanplot of the M-values for a selected sample(/s) for plotSamples.

Author(s)

Matt Ritchie and Cynthia Liu

See Also

genotype.Illumina

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
## Not run: 
   crlmmResult <- genotype.Illumina(sampleSheet=samples[1:10,], path=path,
                                        arrayInfoColNames=list(barcode=NULL,
                                        position="SentrixPosition"),
                                        saveDate=TRUE, cdfName="human370v1c")
   par(mfrow=c(2,2))
   plotSamples(crlmmResult, col=1:4)
   plotSNPs(crlmmResult, row=1:4)

## End(Not run)

benilton/crlmm documentation built on Dec. 27, 2019, 12:12 a.m.