GGtools-package         GGtools Package Overview
X2chunk                 compute numerical matrix of chisq statistics in
                        a genomic interval; extract features as
                        requested
cisProxScores           create, combine, and harvest eqtlTestsManager
                        instances to collect all eQTL tests satisfying
                        certain gene proximity conditions
cisProxScores-class     Class "cisProxScores"
clipPCs                 simple approach to removal of principal
                        components from smlSet
degnerASE01             transcription of a table from a paper by Degner
                        et al
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
externalize             create R package with decomposable smlSet
                        representation
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       snpStats-generated rules from imputing from
                        HapMap phase III loci to 1000 genomes loci -
                        for chromosome 20 only
m20                     snpStats (1.1.1) 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
mkCisTransDirector      Create an object that manages a collection of
                        eqtlTestManagers
multffCT                parallelized multipopulation cis-trans eQTL
                        searches
multiCisDirector-class
                        Class "multiCisDirector"
pcChooser               utility to assist in choosing number of PCs to
                        remove owing to expression heterogeneity
permEx                  permute expression data against genotype data
                        in an smlSet
plot,cwSnpScreenResult,missing-method
                        Methods for Function plot in Package 'GGtools'
relocate                assist in the transport between systems of ff
                        data managed by GGtools
strMultPop              serialization of a table from Stranger's
                        multipopulation eQTL report
topSnps-methods         report on most significant SNP with gwSnpTests
                        results
vcf2sm                  generate a SnpMatrix instance on the basis of a
                        VCF (4.0) file
