# software and data for genetical genomics (c) 2006 VJ Carey

## Documentation for package `GGtools' version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

chr20GGdem | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
chr20meta | Class "snpMeta" - HapMap-based metadata structures for SNPs
chromosome,snpMeta-method | Class "snpMeta" - HapMap-based metadata structures for SNPs
coerce,snpMeta,data.frame-method | Class "snpMeta" - HapMap-based metadata structures for SNPs
countRare | compute rare allele count from a hapmap file
df2snpMeta | compute rare allele count from a hapmap file
dim,snpMeta-method | Class "snpMeta" - HapMap-based metadata structures for SNPs
exclMono | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
extract_p | compute model fits over a sequence of SNPs
fastAGM | compute model fits over a sequence of SNPs
fastHET | compute model fits over a sequence of SNPs
geneLocs | gene metadata from NCBI
genesym | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
genesym-class | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
genoStrings | create a character vector of genotype value strings
getpsid | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
getRare | compute rare allele count from a hapmap file
hgfocusSYMMEMO | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
HM2rac | compute rare allele count from a hapmap file
HMworkflow | function to bind together HapMap genotyping results and expression data
litex | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
litsn | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
make_racExSet | create a racExSet from simpler constituents
nrow,snpMeta-method | Class "snpMeta" - HapMap-based metadata structures for SNPs
oneFit | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
oneFit,racExSet,character,character,function-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
oneFit,racExSet,genesym,character,function-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
oneFit,racExSet,list,character,function-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
oneFit,racExSet,list,formula,function-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
oneFit,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
pdd | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
plot_EvG | plot expression vs genotype
plot_mlp | compute model fits over a sequence of SNPs
racAssays | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
racAssays,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
racExSet-class | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
rarebase | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
rarebase,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
rb20M | create a racExSet from simpler constituents
Sa20M | create a racExSet from simpler constituents
show,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
show,snpMeta-method | Class "snpMeta" - HapMap-based metadata structures for SNPs
show,snpScreenResult-method | compute model fits over a sequence of SNPs
SNPalleles | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
SNPalleles,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snpID | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snpID-class | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snpMeta-class | Class "snpMeta" - HapMap-based metadata structures for SNPs
snpNames | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snpNames,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snps | accessor for genotype data in a ggExprSet
snps,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snps3PrimeTo | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snps5PrimeTo | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
snpScreen | compute model fits over a sequence of SNPs
snpScreen,racExSet,snpMeta,genesym,formula,function,numeric-method | compute model fits over a sequence of SNPs
snpScreenResult-class | compute model fits over a sequence of SNPs
snpsNear | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
thinHM2meta | compute rare allele count from a hapmap file
thinHM2rac | compute rare allele count from a hapmap file
[,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
[,snpMeta-method | Class "snpMeta" - HapMap-based metadata structures for SNPs