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

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Documentation for package ‘GGtools’ version 3.6.1

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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
cisSnpTests perform tests for eQTL cis to specified genes
coerce-method Transform results of gwSnpTests to browser tracks
diagffCC perform a 'diagonal' cis eQTL search (only check SNPs chromosomally coresident with genes)
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)
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
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
maxchisq Class "maxchisq"
maxchisq-class Class "maxchisq"
min_p_vals Class "maxchisq"
min_p_vals-method Class "maxchisq"
multffCT parallelized multipopulation cis-trans eQTL searches
multffManager-class Class "multffManager"
plot-method Methods for Function plot in Package '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 "maxchisq"
show-method Class "multffManager"
snp130locs prototypical function for creation of IRanges-based SNP location data
snpLocs20 prototype SNP location instance for use with GGtools
strMultPop serialization of a table from Stringer's multipopulation eQTL report
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
[-method Class "multffManager"