gQTLs: use SummarizedExperiment to manage a collection of gQTL...

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

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

Note

very preliminary

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")

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