eqBox: descriptive plot of expression against genotype for cisAssoc...
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Details Value Examples

descriptive plot of expression against genotype for cisAssoc results

1 2	eqBox(gene, snp, se, tf, radius=1e6, genome="hg19", ...) eqDesc(gene, snp, se, tf, radius=1e6, genome="hg19", ...)

`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

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

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

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 )
 }