eqBox2: visualization of expression or other assay measure against...

In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

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 )

gQTLstats documentation built on Nov. 8, 2020, 7:53 p.m.