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
dropMonomorphies        remove monomorphic loci from an smlSet instance
eqtlEstimatesManager-class
                        Class '"eqtlEstimatesManager"'
eqtlFDRtab-class        Class '"eqtlFDRtab"'
eqtlTests               perform genome x transcriptome eQTL searches
                        with high-performance options
eqtlTestsManager-class
                        Class "eqtlTestsManager"
ex                      two chromosomes of genotype data and full
                        expression data for CEPH CEU hapmap data
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
geneIndcol              tools for working with transManager instances
genewiseFDRtab          encapsulates testing, permutation and
                        thresholding using permutation distribution to
                        obtain plug-in estimates of FDR at various
                        thresholds
gwSnpTests              methods for iterating association tests
                        (expression vs SNP) across genomes or
                        chromosomes
hla2set                 a gene set of 9 genes from human HLA2 locus
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
mrefhap2sm              transform MACH-supplied haplotype data for
                        imputation into a SnpMatrix instance
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'
probeLocations          utilities for annotation acquisition with
                        smlSet instances
relocate                assist in the transport between systems of ff
                        data managed by GGtools
sm2ped                  create a data.frame representing a PED file
                        (MACH) from a SnpMatrix instance
strMultPop              serialization of a table from Stranger's
                        multipopulation eQTL report
topSnps-methods         report on most significant SNP with gwSnpTests
                        results
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
