# software and data for genetics of gene expression (c) 2006 VJ Carey

## Documentation for package ‘GGtools’ version 4.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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"