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


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Documentation for package ‘GGBase’ version 3.0.0

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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
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
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
gwSnpScreenResult-class Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects
hsSnpLocs SNP location accessor
multiGwSnpScreenResult-class Class "gwSnpScreenResult" - containers for GGtools gwSnpScreen method outputs and allied objects
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
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,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,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-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
snp.rhs.tests154 Score tests with SNP genotypes as independent variable - taken from snpMatrix 1.5.4 while 1.5.5 version of this function is diminished in speed
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
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
[,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