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| GGtools-package | GGtools Package Overview |
| checkCommonSNPs | 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 |
| chunksize | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| chunksize-class | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| cisProxScores | create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions |
| cisProxScores-class | Class "cisProxScores" |
| cisTransDirector-class | Class "eqtlTestsManager" |
| 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 |
| eqtlEstimates | perform genome x transcriptome eQTL searches with high-performance options |
| 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 |
| geneNames | 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 |
| getGene2SnpList | utilities for annotation acquisition with smlSet instances |
| GGtools | GGtools Package Overview |
| gwSnpTests | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| hla2set | a gene set of 9 genes from human HLA2 locus |
| ieqtlTests | perform genome x transcriptome eQTL searches with high-performance options |
| imphm3_1KG_20_mA2 | snpStats-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only |
| imphm3_1KG_20_mA5 | snpStats-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only |
| interleave2cis | create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions |
| locusNames | tools for working with transManager instances |
| 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 |
| makeDiagDirector | Class "multiCisDirector" |
| 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 |
| mtransScores | obtain the top trans associations for each SNP in an smlSet |
| multiCisDirector-class | Class "multiCisDirector" |
| nthScores | tools for working with transManager instances |
| 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-method | Methods for Function plot in Package 'GGtools' |
| policywiseFDRtab | encapsulates testing, permutation and thresholding using permutation distribution to obtain plug-in estimates of FDR at various thresholds |
| probeChromosomes | utilities for annotation acquisition with smlSet instances |
| probeLocations | utilities for annotation acquisition with smlSet instances |
| probeNames | Class "eqtlTestsManager" |
| probeNames-method | Class "eqtlTestsManager" |
| probeSequences | utilities for annotation acquisition with smlSet instances |
| probesManaged | Class "eqtlTestsManager" |
| probesManaged-method | Class "eqtlTestsManager" |
| proximityList | utilities for annotation acquisition with smlSet instances |
| relocate | assist in the transport between systems of ff data managed by GGtools |
| residTests | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| residTests-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| restrictProbesToChrom | utilities for annotation acquisition with smlSet instances |
| scoresByGenes | create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions |
| show-method | Class "cisProxScores" |
| show-method | Class '"eqtlFDRtab"' |
| show-method | Class "eqtlTestsManager" |
| show-method | Class "multiCisDirector" |
| show-method | Class '"transManager"' |
| show-method | generate a SnpMatrix instance on the basis of a VCF (4.0) file |
| sm2ped | create a data.frame representing a PED file (MACH) from a SnpMatrix instance |
| snpLocations | utilities for annotation acquisition with smlSet instances |
| snpsManaged | Class "eqtlTestsManager" |
| snpsManaged-method | Class "eqtlTestsManager" |
| strMultPop | serialization of a table from Stranger's multipopulation eQTL report |
| topFeats | compute numerical matrix of chisq statistics in a genomic interval; extract features as requested |
| topFeats-method | compute numerical matrix of chisq statistics in a genomic interval; extract features as requested |
| topGenes | tools for working with transManager instances |
| topScores | tools for working with transManager instances |
| topSnps | report on most significant SNP with gwSnpTests results |
| topSnps-method | report on most significant SNP with gwSnpTests results |
| topSnps-methods | report on most significant SNP with gwSnpTests results |
| tr1_obs | obtain the top trans associations for each SNP in an smlSet |
| tr1_perm | obtain the top trans associations for each SNP in an smlSet |
| 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 |
| vcf2sm-method | generate a SnpMatrix instance on the basis of a VCF (4.0) file |
| X2chunk | compute numerical matrix of chisq statistics in a genomic interval; extract features as requested |
| [-method | Class '"eqtlEstimatesManager"' |
| [-method | Class "eqtlTestsManager" |