eqBox {GGtools} | R Documentation

## 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

### Details

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

### Value

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

### 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 )
     }

[Package GGtools version 5.18.0 Index]