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| gQTLstats-package | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| AllAssoc | test for variant-expression associations in cis or generally, using VCF |
| cisAssoc | test for variant-expression associations in cis or generally, using VCF |
| cisCount | test for variant-expression associations in cis or generally, using VCF |
| cisEsts | test for variant-expression associations in cis or generally, using VCF |
| clipPCs | transformations of expression data in smlSet instances |
| clipPCs-method | transformations of expression data in smlSet instances |
| collapse_multiPerm | test for variant-expression associations in cis or generally, using VCF |
| describe | Class '"TransStore"' |
| describe-method | Class '"TransStore"' |
| directPlot | visualize relationship between empirical and modeled FDR based on analysis of a gQTL store |
| distToGene | test for variant-expression associations in cis or generally, using VCF |
| enumerateByFDR | filter a ciseStore instance using an FDR threshold |
| eqBox2 | visualization of expression or other assay measure against genotypes extracted from VCF |
| eqBox3 | visualization of expression or other assay measure against genotypes extracted from VCF |
| eqDesc2 | visualization of expression or other assay measure against genotypes extracted from VCF |
| FDRsupp-class | Class '"FDRsupp"' |
| filteredDFwPerm | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| filtFDR | illustration of FDRsupp class |
| getFDRfunc | Class '"FDRsupp"' |
| getFDRfunc-method | Class '"FDRsupp"' |
| getTab | Class '"FDRsupp"' |
| getTab-method | Class '"FDRsupp"' |
| getTransRegistries | harvest contents of a TransStore by rank in associations of features to SNP |
| gQTLs | use SummarizedExperiment to manage a collection of gQTL results of interest |
| gQTLstats | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| gQTLswarm | use SummarizedExperiment to manage a collection of gQTL results of interest |
| 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 |
| pifdr2 | utility for computing plug-in FDR |
| pifdr3 | utility for computing plug-in FDR |
| plot | create a plottable table for eQTL sensitivity analysis visualization |
| plot.senstab | create a plottable table for eQTL sensitivity analysis visualization |
| prep.cisAssocNB | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| qqStore | create a binned QQplot for a sharded store |
| queryVCF | obtain SnpMatrix from VCF genotypes |
| rawFDR | illustration of FDRsupp class |
| regressOut | transformations of expression data in smlSet instances |
| sensByProbe | create a plottable table for eQTL sensitivity analysis visualization |
| senstab | create a plottable table for eQTL sensitivity analysis visualization |
| setFDRfunc | estimate and store function relating association scores to approximate plug-in FDR |
| storeToFDR | extract a vector from store results as ff (out of memory reference); support statistical reductions |
| storeToFDRByProbe | extract a vector from store results as ff (out of memory reference); support statistical reductions |
| storeToHist | extract a vector from store results as ff (out of memory reference); support statistical reductions |
| storeToMaxAssocBySNP | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| storeToQuantiles | extract a vector from store results as ff (out of memory reference); support statistical reductions |
| table_sensobj_thresh | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| 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 |
| transBrowse2 | shiny app to exhibit genotype:genomic feature distributions |
| TransChunk | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| TransChunk-class | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| TransStore | Instance constructor for managing trans gQTL results |
| TransStore-class | Class '"TransStore"' |
| transTable | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| tsByRank | harvest contents of a TransStore by rank in associations of features to SNP |
| tsByRankAccum | harvest contents of a TransStore by rank in associations of features to SNP |
| tsByRankAccum_sing | harvest contents of a TransStore by rank in associations of features to SNP |
| tsByRank_sing | harvest contents of a TransStore by rank in associations of features to SNP |
| tsIndex.reg | Instance constructor for managing trans gQTL results |
| txsPlot | visualize transformed FDR against transformed association statistics |