#' Constant Option
#' @name ID.TYPE.probeID
#' @docType data
ID.TYPE.probeID <- "ProbeID"
#' Constant Option
#' @name ID.TYPE.geneSymbol
#' @docType data
ID.TYPE.geneSymbol <- "GeneSymbol"
#' Constant Option
#' @name ID.TYPE.RefSeqID
#' @docType data
ID.TYPE.RefSeqID <- "RefSeqID"
#' Constant Option
#' @name ID.TYPE.EntrezID
#' @docType data
ID.TYPE.EntrezID <- "EntrezID"
#' Constant Option
#' @name ID.TYPE.all
#' @docType data
ID.TYPE.all <-
c(ID.TYPE.probeID, ID.TYPE.geneSymbol, ID.TYPE.RefSeqID, ID.TYPE.EntrezID)
names(ID.TYPE.all) <-
c("Probe ID", "Gene Symbol", "Reference Sequence ID", "Entrez ID")
#' Constant Option
#' @name SPECIES.human
#' @docType data
SPECIES.human <- "human"
#' Constant Option
#' @name SPECIES.mouse
#' @docType data
SPECIES.mouse <- "mouse"
#' Constant Option
#' @name SPECIES.rat
#' @docType data
SPECIES.rat <- "rat"
#' Constant Option
#' @name SPECIES.all
#' @docType data
SPECIES.all <- c(SPECIES.human, SPECIES.mouse, SPECIES.rat)
names(SPECIES.all) <- SPECIES.all
#' Constant Option
#' @name DTYPE.microarray
#' @docType data
DTYPE.microarray <- "microarray"
#' Constant Option
#' @name DTYPE.RNAseq.count
#' @docType data
DTYPE.RNAseq.count <- "RNAseq-count"
#' Constant Option
#' @name DTYPE.RNAseq.FPKM
#' @docType data
DTYPE.RNAseq.FPKM <- "RNAseq-FPKM/RPKM/TPM"
#' Constant Option
#' @name DTYPE.all
#' @docType data
DTYPE.all <-
c(DTYPE.microarray, DTYPE.RNAseq.count, DTYPE.RNAseq.FPKM)
names(DTYPE.all) <-
c("microarray", "RNAseq-count", "RNAseq-FPKM/RPKM/TPM")
#' Constant Option
#' @name STYPE.multiple
#' @docType data
STYPE.multiple <- "multiple"
#' Constant Option
#' @name STYPE.single
#' @docType data
STYPE.single <- "single"
#' Constant Option
#' @name STYPE.all
#' @docType data
STYPE.all <- c(STYPE.multiple, STYPE.single)
names(STYPE.all) <- c("multiple studies", "single study")
#' Constant Option
#' @name NTYPE.continuous
#' @docType data
NTYPE.continuous <- "continuous"
#' Constant Option
#' @name NTYPE.discrete
#' @docType data
NTYPE.discrete <- "discrete"
#' Constant Option
#' @name NTYPE.all
#' @docType data
NTYPE.all <- c(NTYPE.continuous, NTYPE.discrete)
names(NTYPE.all) <- NTYPE.all
#' Constant Option
#' @name SPECIES.refseq.human
#' @docType data
SPECIES.refseq.human <- "org.Hs.eg.db::org.Hs.egREFSEQ2EG"
#' Constant Option
#' @name SPECIES.refseq.mouse
#' @docType data
SPECIES.refseq.mouse <- "org.Mm.eg.db::org.Mm.egREFSEQ2EG"
#' Constant Option
#' @name SPECIES.refseq.rat
#' @docType data
SPECIES.refseq.rat <- "org.Rn.eg.db::org.Rn.egREFSEQ2EG"
#' Constant Option
#' @name SPECIES.refseq.all
#' @docType data
SPECIES.refseq.all <- c(SPECIES.refseq.human, SPECIES.refseq.mouse, SPECIES.refseq.rat)
names(SPECIES.refseq.all) <- SPECIES.all
#' Constant Option
#' @name SPECIES.entrez.human
#' @docType data
SPECIES.entrez.human <- "org.Hs.eg.db::org.Hs.egSYMBOL"
#' Constant Option
#' @name SPECIES.entrez.mouse
#' @docType data
SPECIES.entrez.mouse <- "org.Mm.eg.db::org.Mm.egSYMBOL"
#' Constant Option
#' @name SPECIES.entrez.rat
#' @docType data
SPECIES.entrez.rat <- "org.Rn.eg.db::org.Rn.egSYMBOL"
#' Constant Option
#' @name SPECIES.entrez.all
#' @docType data
SPECIES.entrez.all <- c(SPECIES.entrez.human, SPECIES.entrez.mouse, SPECIES.entrez.rat)
names(SPECIES.entrez.all) <- SPECIES.all
#' Constant Option
#' @name TO.MATRIX.datasets
#' @docType data
TO.MATRIX.datasets <- "datasets"
#' Constant Option
#' @name TO.MATRIX.clinicals
#' @docType data
TO.MATRIX.clinicals <- "clinicals"
#' Constant Option
#' @name PLATFORM.hgu95a
#' @docType data
PLATFORM.hgu95a <- "hgu95a.db::hgu95aSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu95av2
#' @docType data
PLATFORM.hgu95av2 <- "hgu95av2.db::hgu95av2SYMBOL"
#' Constant Option
#' @name PLATFORM.hgu95b
#' @docType data
PLATFORM.hgu95b <- "hgu95b.db::hgu95bSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu95c
#' @docType data
PLATFORM.hgu95c <- "hgu95c.db::hgu95cSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu95d
#' @docType data
PLATFORM.hgu95d <- "hgu95d.db::hgu95dSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu95e
#' @docType data
PLATFORM.hgu95e <- "hgu95e.db::hgu95eSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu133a
#' @docType data
PLATFORM.hgu133a <- "hgu133a.db::hgu133aSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu133b
#' @docType data
PLATFORM.hgu133b <- "hgu133b.db::hgu133bSYMBOL"
#' Constant Option
#' @name PLATFORM.hgu133plus2
#' @docType data
PLATFORM.hgu133plus2 <- "hgu133plus2.db::hgu133plus2SYMBOL"
#' Constant Option
#' @name PLATFORM.HumanHT.12.V3.Bead.Array
#' @docType data
PLATFORM.HumanHT.12.V3.Bead.Array <- "illuminaHumanv3.db::illuminaHumanv3SYMBOL"
#' Constant Option
#' @name PLATFORM.HumanHT.12.V4.Bead.Array
#' @docType data
PLATFORM.HumanHT.12.V4.Bead.Array <- "illuminaHumanv4.db::illuminaHumanv4SYMBOL"
#' Constant Option
#' @name PLATFORM.HumanWG.6.V1.Bead.Array
#' @docType data
PLATFORM.HumanWG.6.V1.Bead.Array <- "illuminaHumanv1.db::illuminaHumanv1SYMBOL"
#' Constant Option
#' @name PLATFORM.HumanWG.6.V2.Bead.Array
#' @docType data
PLATFORM.HumanWG.6.V2.Bead.Array <- "illuminaHumanv2.db::illuminaHumanv2SYMBOL"
#' Constant Option
#' @name PLATFORM.HumanWG.V2.Bead.Array
#' @docType data
PLATFORM.HumanWG.V2.Bead.Array <- "illuminaHumanv2BeadID.db::illuminaHumanv2BeadIDSYMBOL"
#' Constant Option
#' @name PLATFORM.hgug4100a
#' @docType data
PLATFORM.hgug4100a <- "hgug4100a.db::hgug4100aSYMBOL"
#' Constant Option
#' @name PLATFORM.hgug4101a
#' @docType data
PLATFORM.hgug4101a <- "hgug4101a.db::hgug4101aSYMBOL"
#' Constant Option
#' @name PLATFORM.hgug4110b
#' @docType data
PLATFORM.hgug4110b <- "hgug4110b.db::hgug4110bSYMBOL"
#' Constant Option
#' @name PLATFORM.hgug4111a
#' @docType data
PLATFORM.hgug4111a <- "hgug4111a.db::hgug4111aSYMBOL"
#' Constant Option
#' @name PLATFORM.hgug4112a
#' @docType data
PLATFORM.hgug4112a <- "hgug4112a.db::hgug4112aSYMBOL"
#' Constant Option
#' @name PLATFORM.mgu74a
#' @docType data
PLATFORM.mgu74a <- "mgu74a.db::mgu74aSYMBOL"
#' Constant Option
#' @name PLATFORM.mgu74av2
#' @docType data
PLATFORM.mgu74av2 <- "mgu74av2.db::mgu74av2SYMBOL"
#' Constant Option
#' @name PLATFORM.mgu74b
#' @docType data
PLATFORM.mgu74b <- "mgu74b.db::mgu74bSYMBOL"
#' Constant Option
#' @name PLATFORM.mgu74bv2
#' @docType data
PLATFORM.mgu74bv2 <- "mgu74bv2.db::mgu74bv2SYMBOL"
#' Constant Option
#' @name PLATFORM.mgu74c
#' @docType data
PLATFORM.mgu74c <- "mgu74c.db::mgu74cSYMBOL"
#' Constant Option
#' @name PLATFORM.mgu74cv2
#' @docType data
PLATFORM.mgu74cv2 <- "mgu74cv2.db::mgu74cv2SYMBOL"
#' Constant Option
#' @name PLATFORM.moe430a
#' @docType data
PLATFORM.moe430a <- "moe430a.db::moe430aSYMBOL"
#' Constant Option
#' @name PLATFORM.moe430b
#' @docType data
PLATFORM.moe430b <- "moe430b.db::moe430bSYMBOL"
#' Constant Option
#' @name PLATFORM.GenePLATFORM.Mouse.Genome.430.2.0
#' @docType data
PLATFORM.GenePLATFORM.Mouse.Genome.430.2.0 <- "mouse4302.db::mouse4302SYMBOL"
#' Constant Option
#' @name PLATFORM.MouseWG.6.v1.0.Bead.Array
#' @docType data
PLATFORM.MouseWG.6.v1.0.Bead.Array <- "illuminaMousev1.db::illuminaMousev1SYMBOL"
#' Constant Option
#' @name PLATFORM.MouseWG.6.v2.0.Bead.Array
#' @docType data
PLATFORM.MouseWG.6.v2.0.Bead.Array <- "illuminaMousev2.db::illuminaMousev2SYMBOL"
#' Constant Option
#' @name PLATFORM.mgug4104a
#' @docType data
PLATFORM.mgug4104a <- "mgug4104a.db::mgug4104aSYMBOL"
#' Constant Option
#' @name PLATFORM.mgug4120a
#' @docType data
PLATFORM.mgug4120a <- "mgug4120a.db::mgug4120aSYMBOL"
#' Constant Option
#' @name PLATFORM.mgug4121a
#' @docType data
PLATFORM.mgug4121a <- "mgug4121a.db::mgug4121aSYMBOL"
#' Constant Option
#' @name PLATFORM.mgug4122a
#' @docType data
PLATFORM.mgug4122a <- "mgug4122a.db::mgug4122aSYMBOL"
#' Constant Option
#' @name PLATFORM.rat2302
#' @docType data
PLATFORM.rat2302 <- "rat2302.db::rat2302SYMBOL"
#' Constant Option
#' @name PLATFORM.rgu34a
#' @docType data
PLATFORM.rgu34a <- "rgu34a.db::rgu34aSYMBOL"
#' Constant Option
#' @name PLATFORM.rgu34b
#' @docType data
PLATFORM.rgu34b <- "rgu34b.db::rgu34bSYMBOL"
#' Constant Option
#' @name PLATFORM.rgu34c
#' @docType data
PLATFORM.rgu34c <- "rgu34c.db::rgu34cSYMBOL"
#' Constant Option
#' @name PLATFORM.Rat.v1.0.Bead.Array
#' @docType data
PLATFORM.Rat.v1.0.Bead.Array <- "illuminaRatv1.db::illuminaRatv1SYMBOL"
#' Constant Option
#' @name PLATFORM.rgug4105a
#' @docType data
PLATFORM.rgug4105a <- "rgug4105a.db::rgug4105aSYMBOL"
#' Constant Option
#' @name PLATFORM.rgug4130a
#' @docType data
PLATFORM.rgug4130a <- "rgug4130a.db::rgug4130aSYMBOL"
#' Constant Option
#' @name PLATFORM.rgug4131a
#' @docType data
PLATFORM.rgug4131a <- "rgug4131a.db::rgug4131aSYMBOL"
#' Constant Option
#' @name PLATFORM.all
#' @docType data
PLATFORM.all <- c(
PLATFORM.hgu95a,
PLATFORM.hgu95av2,
PLATFORM.hgu95b,
PLATFORM.hgu95c,
PLATFORM.hgu95d,
PLATFORM.hgu95e,
PLATFORM.hgu133a,
PLATFORM.hgu133b,
PLATFORM.hgu133plus2,
PLATFORM.HumanHT.12.V3.Bead.Array,
PLATFORM.HumanHT.12.V4.Bead.Array,
PLATFORM.HumanWG.6.V1.Bead.Array,
PLATFORM.HumanWG.6.V2.Bead.Array,
PLATFORM.HumanWG.V2.Bead.Array,
PLATFORM.hgug4100a,
PLATFORM.hgug4101a,
PLATFORM.hgug4110b,
PLATFORM.hgug4111a,
PLATFORM.hgug4112a,
PLATFORM.mgu74a,
PLATFORM.mgu74av2,
PLATFORM.mgu74b,
PLATFORM.mgu74bv2,
PLATFORM.mgu74c,
PLATFORM.mgu74cv2,
PLATFORM.moe430a,
PLATFORM.moe430b,
PLATFORM.GenePLATFORM.Mouse.Genome.430.2.0,
PLATFORM.MouseWG.6.v1.0.Bead.Array,
PLATFORM.MouseWG.6.v2.0.Bead.Array,
PLATFORM.mgug4104a,
PLATFORM.mgug4120a,
PLATFORM.mgug4121a,
PLATFORM.mgug4122a,
PLATFORM.rat2302,
PLATFORM.rgu34a,
PLATFORM.rgu34b,
PLATFORM.rgu34c,
PLATFORM.Rat.v1.0.Bead.Array,
PLATFORM.rgug4105a,
PLATFORM.rgug4130a,
PLATFORM.rgug4131a
)
names(PLATFORM.all) <- c(
"chip hgu95a" ,
"chip hgu95av2" ,
"chip hgu95b" ,
"chip hgu95c" ,
"chip hgu95d" ,
"chip hgu95e" ,
"chip hgu133a" ,
"chip hgu133b" ,
"hgu133plus2" ,
"Illumina HumanHT-12 V3 Bead Array" ,
"Illumina HumanHT-12 V4 Bead Array" ,
"Illumina HumanWG-6 V1 Bead Array" ,
"Illumina HumanWG-6 V2 Bead Array" ,
"Illumina HumanWG V2 Bead Array" ,
"chip hgug4100a" ,
"chip hgug4101a" ,
"chip hgug4110b" ,
"chip hgug4111a" ,
"chip hgug4112a" ,
"chip mgu74a" ,
"chip mgu74av2" ,
"chip mgu74b" ,
"chip mgu74bv2" ,
"chip mgu74c" ,
"chip mgu74cv2" ,
"chip moe430a" ,
"chip moe430b" ,
"Affymetrix GeneChip Mouse Genome 430 2.0",
"Illumina MouseWG-6 v1.0 Bead Array" ,
"Illumina MouseWG-6 v2.0 Bead Array" ,
"chip mgug4104a" ,
"chip mgug4120a" ,
"chip mgug4121a" ,
"chip mgug4122a" ,
"chip rat2302" ,
"chip rgu34a" ,
"chip rgu34b" ,
"chip rgu34c" ,
"Illumina Rat v1.0 Bead Array" ,
"chip rgug4105a" ,
"chip rgug4130a" ,
"chip rgug4131a"
)
#' Constant Option
#' @name IMPUTE.method.knn
#' @docType data
IMPUTE.method.knn <- "knn"
#' Constant Option
#' @name IMPUTE.method.remove
#' @docType data
IMPUTE.method.remove <- "remove"
#' Constant Option
#' @name IMPUTE.method.all
#' @docType data
IMPUTE.method.all <- c(IMPUTE.method.knn, IMPUTE.method.remove)
names(IMPUTE.method.all) <- IMPUTE.method.all
#' Constant Option
#' @name REPLICATE.IQR
#' @docType data
REPLICATE.IQR <- "IRQ"
#' Constant Option
#' @name REPLICATE.largest
#' @docType data
REPLICATE.largest <- "largest"
#' Constant Option
#' @name REPLICATE.average
#' @docType data
REPLICATE.average <- "average"
#' Constant Option
#' @name REPLICATE.all
#' @docType data
REPLICATE.all <- c(REPLICATE.IQR, REPLICATE.largest, REPLICATE.average)
names(REPLICATE.all) <- REPLICATE.all
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