infrastructure for genetics of gene expression (c) 2008 VJ Carey


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Documentation for package ‘GGBase’ version 3.6.0

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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