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 |