All.cis                 functions that compute score tests for all SNP
                        cis to genes, with flexible filtering
CisConfig-class         Class '"CisConfig"'
EqAppr-class            Class '"EqAppr"'
GGtools-package         software and data for analyses in genetics of
                        gene expression
TransConfig-class       Class '"TransConfig"'
appraise                appraisal for eQTL prediction models
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
cgff2dt                 translate the GFF3 from a
                        ciseqByCluster/processgff output into a
                        serialized data.table instance, compute
                        genome-wide plug-in FDR, and update the GFF3
                        with this FDR
cisAssoc                test for variant-expression associations in
                        cis, using VCF
cisRun-class            Class '"cisRun"'
ciseqByCluster          end-to-end cluster-based cis-eQTL search, and
                        allied utilities
collectBest             given a collection of All.cis outputs (cisRun
                        instances) compute FDRs for various filterings
concatCis               combine a list of cisRun instances to a single
                        instance
eqBox                   descriptive plot of expression against genotype
                        for cisAssoc results
eqsens_dt               support for sensitivity analyses related to
                        eQTL enumerations
eqtlTests               compute association statistics between all
                        probes and SNP in an smlSet instance
eqtlTests.me            use MatrixEQTL computations and statistics as a
                        back end to GGtools eqtlTests
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
gffprocess              transform a collection of gff3 into a single
                        tabix-indexed gff3
gwSnpTests              execute a series of tests for association
                        between genotype and expression
hmm878                  labeled GRanges with ChromHMM chromatin states
                        for GM12878
meta.bindmaf            bind testing metadata to a best.cis.eQTLs
                        result
pifdr                   utility for computing plug-in FDR
qqhex                   obtain qqplot coordinates for the specific case
                        of comparing a given distribution to that of
                        multiple realizations from a permutation
                        distribution, and bin these coordinates using
                        hexbin, useful for very large samples
richNull                bind metadata concerning SNP allele frequency
                        and other aspects of optimized cis-eQTL
                        association to an mcwBestCis instance
sampsInVCF              enumerate samples available in a VCF file
scoresCis               visualize a gene model with cis-eQTL
                        association scores (-log FDR by default) on the
                        basis of a ciseqByCluster data.table output
sensanal                Summarize information from a collection of eQTL
                        searches for sensitivity assessment
sensiCisInput-class     Class '"sensiCisInput"'
sensiCisOutput-class    Class '"sensiCisOutput"'
simpleTiling            create a GRanges with a tiling of the human
                        genome
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
transeqByCluster        convenience functions for trans-eQTL testing
vcf2sm                  generate a SnpMatrix instance on the basis of a
                        VCF (4.0) file
