GGtools-package         GGtools Package Overview
X2chunk                 compute numerical matrix of chisq statistics in
                        a genomic interval; extract features as
                        requested
bestCis                 extract best (or all) cis-associated eQTL from
                        a multffmgr instance
cisRanges               create GRanges instance for intervals cis to a
                        set of genes
cisSnpTests             perform tests for eQTL cis to specified genes
coerce,cwSnpScreenResult,RangedData-method
                        Transform results of gwSnpTests to browser
                        tracks
degnerASE01             transcription of a table from a paper by Degner
                        et al
diagffCC                perform a 'diagonal' cis eQTL search (only
                        check SNPs chromosomally coresident with genes)
eqtlTests               perform genome x transcriptome eQTL searches
                        with high-performance options
eqtlTestsManager-class
                        Class "eqtlTestsManager"
ex6                     example exon region data
exome_minp              acquire minimum p-value for association between
                        genotype and expression
geneRanges              construct a RangedData instance for genes
                        enumerated according to an annotation .db
                        package
geneTrack               create a RangedData structure with multffCT
                        test results (as -log10 p values by default)
getGRanges              acquire a GRanges instance with eQTL scores for
                        all SNP for a given gene
getNamedLocs            get a named vector of SNP locations
gwSnpTests              methods for iterating association tests
                        (expression vs SNP) across genomes or
                        chromosomes
hla2set                 a gene set of 9 genes from human HLA2 locus
hmceuB36.2021           two chromosomes of genotype data and full
                        expression data for CEPH CEU hapmap data
imphm3_1KG_20_mA2       snpMatrix-generated rules from imputing from
                        HapMap phase III loci to 1000 genomes loci -
                        for chromosome 20 only
m20                     snpMatrix (1.3.13) with imputed genotypes for
                        110 HapMap phase III samples from CEU
                        population
makeCommonSNPs          confine the SNPs (in multiple chromosomes) in
                        all elements of a list of smlSets to the
                        largest shared subset per chromosome; test for
                        satisfaction of this condition
manhPlot                manhattan plot for an eqtlTests result
maxchisq-class          Class "maxchisq"
mkCisTransDirector      Create an object that manages a collection of
                        eqtlTestManagers
multffCT                parallelized multipopulation cis-trans eQTL
                        searches
multffManager-class     Class "multffManager"
permEx                  permute expression data against genotype data
                        in an smlSet
plot,cwSnpScreenResult,missing-method
                        Methods for Function plot in Package 'GGtools'
scoresInRanges          structured survey of eqtlTestsManager to
                        retrieve scores cis to genes
snp130locs              prototypical function for creation of
                        IRanges-based SNP location data
snpLocs20               prototype SNP location instance for use with
                        GGtools
strMultPop              serialization of a table from Stringer's
                        multipopulation eQTL report
topSnps-methods         report on most significant SNP with gwSnpTests
                        results
vcf2sm                  generate a snp.matrix instance on the basis of
                        a VCF (4.0) file
