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

## Documentation for package ‘GGtools’ version 1.6.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

addAnno | Class "oGtypeExSet" ~~~
chr20GGdem | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
chr20meta | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
chromosome,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
coerce,oGtypeExSet,ExpressionSet-method | Class "oGtypeExSet" ~~~
coerce,snpMeta,data.frame-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -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 (or Wellcome INBREDS) -based metadata structures for SNPs
exclMono | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
exprs,racExSet-method | 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 | Class "GGfitter" wrapper for special functions to do whole genome screens
fastAGMfitter | Class "GGfitter" wrapper for special functions to do whole genome screens
fastHET | Class "GGfitter" wrapper for special functions to do whole genome screens
fastHETfitter | Class "GGfitter" wrapper for special functions to do whole genome screens
geneLocs | gene metadata from NCBI
geneLocs_hsa | gene metadata from NCBI
geneLocs_mmu | 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
getSNPindices | Class "oGtypeExSet" ~~~
GGfitter-class | Class "GGfitter" wrapper for special functions to do whole genome screens
gse2031GG | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
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
INB34snpMeta | convert a Wellcome 'Strains' genotyping file to rare allele count form
INBREDSworkflow | convert a Wellcome 'Strains' genotyping file to rare allele count form
initialize,oGtypeExSet-method | Class "oGtypeExSet" ~~~
initialize,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype 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
mgu74av2SYMMEMO | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
nrow,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
oGtypeExSet-class | Class "oGtypeExSet" ~~~
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 "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,oGtypeExSet-method | Class "oGtypeExSet" ~~~
show,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
show,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -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 (or Wellcome INBREDS) -based metadata structures for SNPs
snpMetaWhole | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
snpMetaWhole-class | Class "snpMeta" - HapMap (or Wellcome INBREDS) -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,missing-method | compute model fits over a sequence of SNPs
snpScreen,racExSet,snpMeta,genesym,formula,function,numeric-method | compute model fits over a sequence of SNPs
snpScreen,racExSet,snpMeta,genesym,formula,GGfitter,ANY-method | Class "GGfitter" wrapper for special functions to do whole genome screens
snpScreen,racExSet,snpMeta,genesym,formula,GGfitter-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
Strains2rac | convert a Wellcome 'Strains' genotyping file to rare allele count form
thinHM2meta | compute rare allele count from a hapmap file
thinHM2rac | compute rare allele count from a hapmap file
tx_rsnum | Class "oGtypeExSet" ~~~
wrapSNPmetaWh | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
[,racExSet,ANY,ANY,ANY-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
[,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
[,snpMeta,ANY,ANY,ANY-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
[,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs