gQTLstats (version 1.4.2)

gQTLs: use SummarizedExperiment to manage a collection of gQTL results of interest

Description

use SummarizedExperiment to manage a collection of gQTL results of interest

Usage

gQTLs(filtgr, se, tf, genome = "hg19", forceRs = TRUE, chunksize = 50)
gQTLswarm(se, ind, covar = NULL, inpch = 19, xlab, ylab, featTag="probeid", ...)

Arguments

filtgr

a GRanges instance typically obtained by filtering a ciseStore instance

se

SummarizedExperiment with individual level expression and sample-level data from which filtgr statistics were derived; for gQTLswarm, output of gQTLs

tf

TabixFile for VCF on which filtgr statistics are based

genome

tag for readVcf

forceRs

if TRUE insist that snp ids include 'rs'

chunksize

VCF processing proceeds via foreach in chunks of size chunksize

ind

index into rows of se to be used for visualization, must be length 1

covar

a character string indicating a variable in colData(se) to be used to color the points

inpch

pch setting for dots in swarm

xlab

xlabel for beeswarm plot, defaults to snp id as recovered from rowRanges(se)$snp

ylab

ylabel for beeswarm plot, defaults to probe id as recovered from rowRanges(se)$probeid

featTag

element of mcols(rowRanges(se)) used to find ylab text, defaults to 'probeid', 'symbol' is often preferred

...

passed to beeswarm

Value

• a SummarizedExperiment instance with two assays, the first is genotype the second is expression

Examples

require(Rsamtools)
tf = TabixFile(system.file("vcf/litv.vcf.gz", package="gQTLstats"))
data(sigInlit) # 33 loci with significant cis eQTL on a specific filtering
library(geuvPack)
data(geuFPKM)
require(doParallel)
registerDoSEQ()
gdem = gQTLs(sigInlit, geuFPKM, tf, genome = "hg19")
gQTLswarm(gdem, 1, "popcode")