eqBox {GGtools} | R Documentation |
descriptive plot of expression against genotype for cisAssoc results
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 ) }