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


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Documentation for package ‘GGtools’ version 3.10.2

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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
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
getSS create R package with decomposable smlSet representation
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
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
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
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
mcisProxScores create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions
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-method Methods for Function plot in Package 'GGtools'
probeNames Class "eqtlTestsManager"
probeNames-method Class "eqtlTestsManager"
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
show-method Class "cisProxScores"
show-method Class "eqtlTestsManager"
show-method Class "multiCisDirector"
show-method generate a SnpMatrix instance on the basis of a VCF (4.0) file
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
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
vcf2sm 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 "eqtlTestsManager"