| 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 |
| 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 |
| 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 |
| 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,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 |
| 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 |
| 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 |
| [,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 |