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| GGbase-package | GGbase Package Overview |
| chrnum | Class "genesym" and other casting classes |
| chrnum,character-method | Class "genesym" and other casting classes |
| chrnum,numeric-method | Class "genesym" and other casting classes |
| chrnum-class | Class "genesym" and other casting classes |
| cnumOrMissing | Class "genesym" and other casting classes |
| cnumOrMissing-class | Class "genesym" and other casting classes |
| coerce,smlSet,ExpressionSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| combine,filteredMultiGwSnpScreenResult,filteredMultiGwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| combine,multiGwSnpScreenResult,multiGwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| combine,smlSet,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| cwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| exprs,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| featureFilter | remove unannotated or undesired features from an smlSet instance |
| filteredGwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| filteredMultiGwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| genesym | Class "genesym" and other casting classes |
| genesym,character-method | Class "genesym" and other casting classes |
| genesym-class | Class "genesym" and other casting classes |
| getAlleles | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| getAlleles,smlSet,rsid-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| getSnpLocs | SNP location accessor |
| getSnpLocs,smlSet,chrnum-method | SNP location accessor |
| getSnpLocs,smlSet,missing-method | SNP location accessor |
| GGbase | GGbase Package Overview |
| gwSnpScreenResult | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| gwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| hsSnpLocs | SNP location accessor |
| MAFfilter | restrict SNP in an smlSet to range of minor allele frequencies (MAF) |
| multiCisTestResult-class | Class "multiCisTestResult" |
| multiGwSnpScreenResult-class | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| phenoVar | Class "genesym" and other casting classes |
| phenoVar,character-method | Class "genesym" and other casting classes |
| phenoVar-class | Class "genesym" and other casting classes |
| plot,cwSnpScreenResult,ANY-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| plot,gwSnpScreenResult,ANY-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| plot,multiGwSnpScreenResult,ANY-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| plot_EvG | formal method for visualizing expression distributions vs genotype |
| plot_EvG,genesym,rsid,smlSet-method | formal method for visualizing expression distributions vs genotype |
| plot_EvG,probeId,rsid,smlSet-method | formal method for visualizing expression distributions vs genotype |
| plot_EvG-methods | formal method for visualizing expression distributions vs genotype |
| plot_EvG2 | formal method for visualizing expression distributions vs genotype |
| plot_EvG2,genesym,rsid,rsid,smlSet-method | formal method for visualizing expression distributions vs genotype |
| plot_EvG2,probeId,rsid,rsid,smlSet-method | formal method for visualizing expression distributions vs genotype |
| probeId | Class "genesym" and other casting classes |
| probeId,character-method | Class "genesym" and other casting classes |
| probeId-class | Class "genesym" and other casting classes |
| rsid | Class "genesym" and other casting classes |
| rsid,character-method | Class "genesym" and other casting classes |
| rsid,numeric-method | Class "genesym" and other casting classes |
| rsid-class | Class "genesym" and other casting classes |
| SessionInfo-class | Class "SessionInfo" - objects to help stamp an output with information on session state |
| show,chrnum-method | Class "genesym" and other casting classes |
| show,cwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| show,filteredGwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| show,filteredMultiGwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| show,gwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| show,multiCisTestResult-method | Class "multiCisTestResult" |
| show,multiGwSnpScreenResult-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| show,rsid-method | Class "genesym" and other casting classes |
| show,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| show,smlSummary-method | class and function to summarize frequency information on genotypes in an smlSet |
| show,snpLocs-method | SNP location accessor |
| smlEnv | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| smlEnv,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| smList | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| smList,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| smlSet | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| smlSet-class | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| smlSummary | class and function to summarize frequency information on genotypes in an smlSet |
| smlSummary-class | class and function to summarize frequency information on genotypes in an smlSet |
| snpdepth | Class "genesym" and other casting classes |
| snpdepth-class | Class "genesym" and other casting classes |
| snpLocs-class | SNP location accessor |
| snpLocs.Hs | SNP location accessor |
| snpLocs.Hs,chrnum,missing-method | SNP location accessor |
| snpLocs.Hs,chrnum,rsid-method | SNP location accessor |
| snpLocs.Hs,chrnum.missing-method | SNP location accessor |
| snpLocs.Hs,chrnum.rsid-method | SNP location accessor |
| snpLocs.Hs,missing,rsid-method | SNP location accessor |
| snpLocs.Hs,rsid,ANY-method | SNP location accessor |
| snpLocs.Hs,rsid-method | SNP location accessor |
| snpLocs.Hs,sid,ANY-method | SNP location accessor |
| snpNames | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| snpNames,smlSet,chrnum-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| snpNames,smlSet,missing-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| snps | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| snps,smlSet,chrnum-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| snpsNear | obtain list of rs numbers for snps near a gene |
| [,cwSnpScreenResult,ANY,ANY,ANY-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| [,gwSnpScreenResult,ANY,ANY,ANY-method | Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects |
| [,smlSet,ANY,ANY,ANY-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |
| [,snp.matrix,ANY,rsid,ANY-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes |