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

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Documentation for package ‘GGtools’ version 3.8.4

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GGtools-package GGtools Package Overview
bestCis extract best (or all) cis-associated eQTL from a multffmgr instance
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
cisRanges create GRanges instance for intervals cis to a set of genes
cisScores perform genome x transcriptome eQTL searches with high-performance options
cisSnpTests perform tests for eQTL cis to specified genes
cisTransDirector-class Class "eqtlTestsManager"
coerce-method Class "multffManager"
coerce-method Transform results of gwSnpTests to browser tracks
degnerASE01 transcription of a table from a paper by Degner et al
diagffCC perform a 'diagonal' cis eQTL search (only check SNPs chromosomally coresident with genes)
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
geneRanges construct a RangedData instance for genes enumerated according to an annotation .db package
geneTrack create a RangedData structure with multffCT test results (as -log10 p values by default)
getGRanges acquire a GRanges instance with eQTL scores for all SNP for a given gene
getNamedLocs get a named vector of SNP locations
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
ieqtlTests perform genome x transcriptome eQTL searches with high-performance options
imphm3_1KG_20_mA2 snpMatrix-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only
imphm3_1KG_20_mA5 snpMatrix-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only
m20 snpMatrix (1.3.13) 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
maxchisq Class "maxchisq"
maxchisq-class Class "maxchisq"
meqtlTests perform genome x transcriptome eQTL searches with high-performance options
min_p_vals Class "maxchisq"
min_p_vals-method Class "maxchisq"
mkCisTransDirector Create an object that manages a collection of eqtlTestManagers
multffCT parallelized multipopulation cis-trans eQTL searches
multffManager-class Class "multffManager"
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"
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
scoresInRanges structured survey of eqtlTestsManager to retrieve scores cis to genes
show-method Class "eqtlTestsManager"
show-method Class "maxchisq"
show-method Class "multffManager"
show-method generate a snp.matrix instance on the basis of a VCF (4.0) file
snp130locs prototypical function for creation of IRanges-based SNP location data
snpLocs20 prototype SNP location instance for use with GGtools
snpLocs_21 prototype SNP location instance for use with GGtools
strMultPop serialization of a table from Stringer'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 snp.matrix 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"
[-method Class "multffManager"