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


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Documentation for package ‘GGtools’ version 2.0.2

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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