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


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Documentation for package `GGtools' version 1.4.0

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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 compute model fits over a sequence of SNPs
fastHET compute model fits over a sequence of SNPs
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
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
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
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