# gQTLstats: computationally efficient analysis for eQTL and allied studies

## Documentation for package ‘gQTLstats’ version 1.12.0

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

## Help Pages

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