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 |