GGtools (version 5.8.0)

eqBox: descriptive plot of expression against genotype for cisAssoc results

Description

descriptive plot of expression against genotype for cisAssoc results

Usage

eqBox(gene, snp, se, tf, radius=1e6, genome="hg19", ...)
eqDesc(gene, snp, se, tf, radius=1e6, genome="hg19", ...)

Arguments

gene

identifier of gene in SummarizedExperiment se, must be present in rownames(se)

snp

identifier of variant in VCF referenced by tf

se

SummarizedExperiment instance

tf

TabixFile reference for a VCF file that has been bgzipped and tabix-indexed

radius

in order to limit the VCF import, we filter variants to those within a radius around the selected gene -- it is assumed that the selected snp will exist in that region (we can't extract SNP by name from vcf...)

genome

a simple genome identifier tag

...

(not used with eqDesc) will embellish plot; xlab and ylab already taken care of

Value

eqBox produces a boxplot for all categories (including NA) of genotype. eqDesc tabulates the genotype calls in categories.

Details

The chromosome names in the VCF and the seqlevelsStyle of the Summarized Experiment must match.

Examples

if (require(VariantAnnotation)) {
 data(lgeu)
 lgeue = lgeu[,which(lgeu$popcode=="CEU")]
 tf20 = TabixFile(system.file("vcf/c20exch.vcf.gz", package="GGtools"))
 eqBox( "ENSG00000126005.10", "rs2425038", lgeue, tf20 )
 }