FDRsupp-class           Class '"FDRsupp"'
TransStore              Instance constructor for managing trans gQTL
                        results
TransStore-class        Class '"TransStore"'
cisAssoc                test for variant-expression associations in cis
                        or generally, using VCF
clipPCs                 transformations of expression data in smlSet
                        instances
directPlot              visualize relationship between empirical and
                        modeled FDR based on analysis of a gQTL store
enumerateByFDR          filter a ciseStore instance using an FDR
                        threshold
eqBox2                  visualization of expression or other assay
                        measure against genotypes extracted from VCF
filtFDR                 illustration of FDRsupp class
gQTLs                   use SummarizedExperiment to manage a collection
                        of gQTL results of interest
gQTLstats-package       gQTLstats: computationally efficient analysis
                        for eQTL and allied studies
hmm878                  labeled GRanges with ChromHMM chromatin states
                        for GM12878
manhWngr                manhattan plot with named GRanges
mixedVCFtoSnpMatrix     amalgamate called genotypes and imputed allelic
                        dosages in VCF to SnpMatrix representation
pifdr                   utility for computing plug-in FDR
qqStore                 create a binned QQplot for a sharded store
queryVCF                obtain SnpMatrix from VCF genotypes
senstab                 create a plottable table for eQTL sensitivity
                        analysis visualization
setFDRfunc              estimate and store function relating
                        association scores to approximate plug-in FDR
storeToQuantiles        extract a vector from store results as ff (out
                        of memory reference); support statistical
                        reductions
tqbrowser               general browsing facility for trans-gQTL
transAssoc              compute 'trans' SNP-feature associations by
                        wrapping AllAssoc
transBrowse             shiny app to exhibit genotype:genomic feature
                        distributions
tsByRank                harvest contents of a TransStore by rank in
                        associations of features to SNP
txsPlot                 visualize transformed FDR against transformed
                        association statistics
