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

## Documentation for package ‘GGtools’ version 2.0.2

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A C D E F G H I L M N O P R S T U W misc

## -- A --

addAnno | Class "oGtypeExSet" ~~~
annotation,snpScreenResult-method | compute model fits over a sequence of SNPs

## -- C --

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
chrnum | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
chrnum,numeric-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
chrnum-class | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
chromosome | 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
cnumOrMissing-class | genome-wide test for association between SNP and phenotype
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
cwSnpScreen | genome-wide test for association between SNP and phenotype
cwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics

## -- D --

df2snpMeta | compute rare allele count from a hapmap file
dim,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs

## -- E --

exclMono | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
exFeatID | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
exFeatID-class | 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
exprs,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
extract_p | compute model fits over a sequence of SNPs

## -- F --

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

## -- G --

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
getAbsSnpLocs | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
getAbsSnpLocs,cwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
getAlleles | plot expression vs. genotype
getAlleles,smlSet,rsNum-method | plot expression vs. genotype
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
getSnpChroms | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpChroms,smlSet,logical-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpChroms,smlSet,missing-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpChroms,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpChroms,SQLiteConnection,character-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpData | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpData,character,character-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpData,character-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpData,snpLocNCref-method | Class "snpLocNCref" container for netCDF reference to snp location data
getSNPindices | Class "oGtypeExSet" ~~~
getSnpLocs | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpLocs,smlSet,logical-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpLocs,smlSet,missing-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpLocs,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
getSnpLocs,SQLiteConnection,character-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
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
gwSnpScreen | genome-wide test for association between SNP and phenotype
gwSnpScreen,GeneSet,smlSet,cnumOrMissing-method | genome-wide test for association between SNP and phenotype
gwSnpScreen,genesym,smlSet,cnumOrMissing-method | genome-wide test for association between SNP and phenotype
gwSnpScreen,genesym,smlSet-method | genome-wide test for association between SNP and phenotype
gwSnpScreen-methods | genome-wide test for association between SNP and phenotype
gwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics

## -- H --

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
hmceuB36.2021 | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
HMworkflow | function to bind together HapMap genotyping results and expression data

## -- I --

imputeSNPFixed | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
imputeSNPFixed,racExSet,missing-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
imputeSNPFixed,racExSet,numeric-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype 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

## -- L --

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

## -- M --

make_racExSet | create a racExSet from simpler constituents
mgu74av2SYMMEMO | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
multiGwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics

## -- N --

nrow,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
nsamp | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
nsamp,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package

## -- O --

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

## -- P --

pdd | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
plot,cwSnpScreenResult,ANY-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
plot,cwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
plot,gwSnpScreenResult,ANY-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
plot,gwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
plot_EvG | plot expression vs. genotype
plot_EvG,genesym,rsNum,smlSet-method | plot expression vs. genotype
plot_EvG-methods | plot expression vs. genotype
plot_mlp | compute model fits over a sequence of SNPs
pos | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
pos,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs

## -- R --

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
rawSNP | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
rawSNP,smlSet,numeric-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
rb20M | create a racExSet from simpler constituents
rsNum | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
rsNum,character-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
rsNum-class | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package

## -- S --

Sa20M | create a racExSet from simpler constituents
sampleNames,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
show,gwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
show,multiGwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
show,oGtypeExSet-method | Class "oGtypeExSet" ~~~
show,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
show,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
show,snpLocNCref-method | Class "snpLocNCref" container for netCDF reference to snp location 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
show,twSnpScreenResult-method | compute model fits over a sequence of SNPs
smlEnv,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
smList | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
smList,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
smlSet-class | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
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
snpLocNCref-class | Class "snpLocNCref" container for netCDF reference to snp location 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,missing-method | 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
snps,smlSet,chrnum-method | accessor for genotype data in a ggExprSet
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

## -- T --

thinHM2meta | compute rare allele count from a hapmap file
thinHM2rac | compute rare allele count from a hapmap file
topSnps | report on the smallest p-values for SNP-expression associations
topSnps,cwSnpScreenResult-method | report on the smallest p-values for SNP-expression associations
topSnps,gwSnpScreenResult-method | report on the smallest p-values for SNP-expression associations
topSnps-methods | report on the smallest p-values for SNP-expression associations
twSnpScreen | compute model fits over a sequence of SNPs
twSnpScreen,racExSet,snpMeta,formula,GGfitter-method | compute model fits over a sequence of SNPs
twSnpScreenResult-class | compute model fits over a sequence of SNPs
tx_rsnum | Class "oGtypeExSet" ~~~

## -- U --

updateObject,racExSet-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data

## -- W --

wrapSNPmetaWh | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs

## -- misc --

[,gwSnpScreenResult,ANY,ANY-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
[,gwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for genome-wide and chromosome-wide snp screen statistics
[,racExSet,ANY,ANY,ANY-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
[,racExSet,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
[,smlSet,ANY,ANY-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
[,smlSet-method | Class "smlSet" - efficient representation of SNP+expression data, based on Clayton snpMatrix package
[,snpMeta,ANY,ANY,ANY-method | Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
[,snpMeta,ANY,ANY-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
[,snpMeta-method | Class "snpMeta" - HapMap (or Wellcome INBREDS) -based metadata structures for SNPs