AllelicImbalance (version 1.10.2)

barplot-lattice-support: lattice barplot inner functions for ASEset objects

Description

Generates lattice barplots for ASEset objects. Two levels of plotting detail are provided: a detailed barplot of read counts by allele useful for fewer samples and SNPs, and a less detailed barplot of the fraction of imbalance, useful for more samples and SNPs.

Usage

barplotLatticeFraction(identifier, ...)
barplotLatticeCounts(identifier, ...)

Arguments

identifier,

the single snp name to plot

...

used to pass on variables

Details

filter.pValue.fraction is intended to remove p-value annotation with very large difference in frequency, which could just be a sequencing mistake. This is to avoid p-values like 1e-235 or similar.

sampleColourUser specified colours, either given as named colours ('red', 'blue', etc) or as hexadecimal code. Can be either length 1 for all samples, or else of a length corresponding to the number of samples for individual colouring.

See Also

• The ASEset class which the barplot function can be called up on.

Examples

a <- ASEset
name <- rownames(a)[1]

barplotLatticeFraction(identifier=name, x=a, astrand="+") 
barplotLatticeCounts(identifier=name,  x=a, astrand="+")