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| 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 |