# gQTLstats: computationally efficient analysis for eQTL and allied studies

## Documentation for package ‘gQTLstats’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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