All.cis                 function that computes score tests for all SNP
                        cis to genes, with flexible filtering
CisConfig-class         Class '"CisConfig"'
GGtools-package         software and data for analyses in genetics of
                        gene expression
b1                      mcwBestCis instances, integrative analysis
                        output containers generated by GGtools vignette
best.cis.eQTLs          collect genewise best scoring eQTL
best.trans.eQTLs        collect strongest trans SNP-gene associations
                        in a buffer of size K genes per SNP
bindmaf                 bind testing metadata to a best.cis.eQTLs
                        result
cisRun-class            Class '"cisRun"'
collectBest             given a collection of All.cis outputs (cisRun
                        instances) compute FDRs for various filterings
eqtlTests               compute association statistics between all
                        probes and SNP in an smlSet instance
eqtlTestsManager-class
                        Class '"eqtlTestsManager"'
ex                      ExpressionSet instance for illustrating
                        integrative smlSet container
getCisMap               create, using Bioconductor annotation
                        resources, a structure that enumerates SNP in
                        the vicinity of ('cis' to) genes
gwSnpTests              execute a series of tests for association
                        between genotype and expression
pifdr                   utility for computing plug-in FDR
richNull                bind metadata concerning SNP allele frequency
                        and other aspects of optimized cis-eQTL
                        association to an mcwBestCis instance
sensanal                Summarize information from a collection of eQTL
                        searches for sensitivity assessment
sensiCisInput-class     Class '"sensiCisInput"'
sensiCisOutput-class    Class '"sensiCisOutput"'
snplocsDefault          name the default SNPlocs.Hsapiens.dbSNP.*
                        package
strMultPop              serialization of a table from Stranger's
                        multipopulation eQTL report
transManager-class      Class '"transManager"'
transScores             obtain the top trans associations for each SNP
                        in an smlSet
transTab                tabulate results of transScores run
vcf2sm                  generate a SnpMatrix instance on the basis of a
                        VCF (4.0) file
