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

Description Usage Arguments Details Author(s) See Also Examples

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

1
2
3

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.

Author(s)

Jesper R. Gadin, Lasse Folkersen

See Also

Examples

1
2
3
4
5
a <- ASEset
name <- rownames(a)[1]

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

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.