gQTLs {gQTLstats} | R Documentation |
use SummarizedExperiment to manage a collection of gQTL results of interest
gQTLs(filtgr, se, tf, genome = "hg19", forceRs = TRUE, chunksize = 50) gQTLswarm(se, ind, covar = NULL, inpch = 19, xlab, ylab, featTag="probeid", ...)
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 |
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 |
a SummarizedExperiment instance with two assays, the first is genotype the second is expression
very preliminary
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")