eqBox2 {gQTLstats} | R Documentation

## visualization of expression or other assay measure against genotypes extracted from VCF

### Description

visualization of expression or other assay measure against genotypes extracted from VCF

### Usage

    eqBox2(gene, se, tf, snpgr, genome = "hg19", forceRs=TRUE, ...)
    eqDesc2(gene, se, tf, snpgr, genome = "hg19", forceRs=TRUE)
    eqBox3(gene, se, tf, snpgr, geneAnno, genome = "hg19", forceRs = TRUE,
        ...)

### Arguments

`gene` | an element of rownames(se) from which a vector of assay values will be created
`se` | a `RangedSummarizedExperiment` object
`tf` | instance of class `TabixFile-class`, defining paths to a tabix-indexed VCF and index file
`snpgr` | instance of `GRanges-class` identifying the SNP to be visualized
`genome` | tag identifying reference genome
`forceRs` | In the 1000 genomes VCF, there are sometimes variants identified with DELLY that are grabbed by readVcf on an SNV address. Set forceRs to TRUE to retain only variants with 'rs' in the name. Has no effect if readVcf extracts only a single variant.
`geneAnno` | named vector, `geneAnno[gene]` will be used to annotate display
`...` | extra arguments passed to beeswarm

### Details

In 1.5.4, altered to supply beeswarm data visualization in addition to boxplot. Use additional option corral="gutter" to reduce horizontal sprawl in large samples.

### Examples

    require(Rsamtools)
    require(SummarizedExperiment)
    mygr = GRanges("1", IRanges(54683925, width=1))
    gene = "ENSG00000231581.1"
    library(geuvPack)
    data(geuFPKM)
    #tf = gtpath(1)
    tf = TabixFile(system.file("vcf/small_1.vcf.gz", package="gQTLstats"))
    eqBox2(gene, se=geuFPKM, tf, mygr )
    eqDesc2(gene, se=geuFPKM, tf, mygr )

[Package gQTLstats version 1.12.0 Index]