Man pages for gQTLstats
gQTLstats: computationally efficient analysis for eQTL and allied studies
| cisAssoc | test for variant-expression associations in cis or generally,... |
| clipPCs | transformations of expression data in smlSet instances |
| directPlot | visualize relationship between empirical and modeled FDR... |
| enumerateByFDR | filter a ciseStore instance using an FDR threshold |
| eqBox2 | visualization of expression or other assay measure against... |
| FDRsupp-class | Class '"FDRsupp"' |
| filtFDR | illustration of FDRsupp class |
| gQTLs | use SummarizedExperiment to manage a collection of gQTL... |
| gQTLstats-package | gQTLstats: computationally efficient analysis for eQTL and... |
| hmm878 | labeled GRanges with ChromHMM chromatin states for GM12878 |
| manhWngr | manhattan plot with named GRanges |
| mixedVCFtoSnpMatrix | amalgamate called genotypes and imputed allelic dosages in... |
| 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... |
| setFDRfunc | estimate and store function relating association scores to... |
| storeToStats | extract a vector from store results as ff (out of memory... |
| 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 |
| TransStore | Instance constructor for managing trans gQTL results |
| TransStore-class | Class '"TransStore"' |
| tsByRank | harvest contents of a TransStore by rank in associations of... |
| txsPlot | visualize transformed FDR against transformed association... |
