geuvEvH: compute a data.frame with GEUVADIS expression for a selected...

In vjcitn/BiocRnaHap: explore RNA-seq based haplotyping using Phaser

Description

compute a data.frame with GEUVADIS expression for a selected gene and associated haplotypes formed using entries in snps

Usage

geuvEvH(sym = "GSDMB", snps = c("rs2305480", "rs2305479"),
  vcf = NULL, ...)

Arguments

sym	a character(1) gene symbol
snps	a vector of SNP identifiers
vcf	a CompressedVcf instance from VariantAnnotation
...	not currently used

Note

it is assumed that the entries in 'snps' are elements of a 'long-range' RNA-based haplotype as inferred by phaser

Examples

requireNamespace("geuvPack")
if (!exists("geuFPKM")) {
  require(geuvPack)
  data(geuFPKM)
  }
tab = geuvEvH(vcf=BiocRnaHap::gsd_vcf)
head(tab)
require(ggplot2)
ggplot(tab, aes(x=haplotypes, y=exprs, colour=popcode)) + 
  geom_boxplot(aes(group=haplotypes), outlier.size=0) + 
  geom_jitter() 

vjcitn/BiocRnaHap documentation built on June 17, 2019, 9:31 p.m.