![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| gQTLstats-package | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| cisAssoc | test for variant-expression associations in cis, using VCF |
| clipPCs | transformations of expression data in smlSet instances |
| clipPCs-method | 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 |
| eqDesc2 | visualization of expression or other assay measure against genotypes extracted from VCF |
| FDRsupp-class | Class '"FDRsupp"' |
| filtFDR | illustration of FDRsupp class |
| getFDRfunc | Class '"FDRsupp"' |
| getFDRfunc-method | Class '"FDRsupp"' |
| getTab | Class '"FDRsupp"' |
| getTab-method | Class '"FDRsupp"' |
| gQTLstats | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| hmm878 | labeled GRanges with ChromHMM chromatin states for GM12878 |
| manhWngr | manhattan plot with named GRanges |
| 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 |
| 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 |
| txsPlot | visualize transformed FDR against transformed association statistics |