FDRsupp-class           Class '"FDRsupp"'
cisAssoc                test for variant-expression associations in
                        cis, 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
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
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
txsPlot                 visualize transformed FDR against transformed
                        association statistics
