gQTLstats (version 1.4.2)

eqBox2: 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)

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.

...

extra arguments passed to boxplot

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 )