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

## Documentation for package ‘GGBase’ version 3.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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