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

## Documentation for package ‘GGtools’ version 3.6.1

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

## Help Pages

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"