Man pages for metaOmic/preproc
Preprocessing of Normalized Gene Expression Data
| Annotate | Gene annotation |
| Annotate-matrix-method | Title Annotate Gene Expression Matrix |
| Annotate-Study-method | Title Annotate Study |
| DTYPE.all | Constant Option |
| DTYPE.continuous | Constant Option |
| DTYPE.discrete | Constant Option |
| DTYPE.microarray | Constant Option |
| DTYPE.RNAseq.count | Constant Option |
| DTYPE.RNAseq.FPKM | Constant Option |
| Filter | Filter genes |
| ID.TYPE.all | Constant Option |
| ID.TYPE.EntrezID | Constant Option |
| ID.TYPE.geneSymbol | Constant Option |
| ID.TYPE.probeID | Constant Option |
| ID.TYPE.RefSeqID | Constant Option |
| Impute | Impute missing values |
| Impute-matrix-method | Title Impute Gene Expression Matrix |
| IMPUTE.method.all | Constant Option |
| IMPUTE.method.knn | Constant Option |
| IMPUTE.method.remove | Constant Option |
| Impute-Study-method | Title Impute Study |
| is.continuous | Title is.discrete |
| is.discrete | Title is.discrete |
| Merge | Merge microarray data sets |
| meta | Title Generic Function: meta |
| meta-methods | meta method |
| ntype | Title Generic Function: ntype |
| NTYPE.all | Constant Option |
| NTYPE.continuous | Constant Option |
| NTYPE.discrete | Constant Option |
| ntype-methods | ntype method |
| PLATFORM.all | Constant Option |
| PLATFORM.GenePLATFORM.Mouse.Genome.430.2.0 | Constant Option |
| PLATFORM.hgu133a | Constant Option |
| PLATFORM.hgu133b | Constant Option |
| PLATFORM.hgu133plus2 | Constant Option |
| PLATFORM.hgu95a | Constant Option |
| PLATFORM.hgu95av2 | Constant Option |
| PLATFORM.hgu95b | Constant Option |
| PLATFORM.hgu95c | Constant Option |
| PLATFORM.hgu95d | Constant Option |
| PLATFORM.hgu95e | Constant Option |
| PLATFORM.hgug4100a | Constant Option |
| PLATFORM.hgug4101a | Constant Option |
| PLATFORM.hgug4110b | Constant Option |
| PLATFORM.hgug4111a | Constant Option |
| PLATFORM.hgug4112a | Constant Option |
| PLATFORM.HumanHT.12.V3.Bead.Array | Constant Option |
| PLATFORM.HumanHT.12.V4.Bead.Array | Constant Option |
| PLATFORM.HumanWG.6.V2.Bead.Array | Constant Option |
| PLATFORM.HumanWG.V2.Bead.Array | Constant Option |
| PLATFORM.mgu74a | Constant Option |
| PLATFORM.mgu74av2 | Constant Option |
| PLATFORM.mgu74b | Constant Option |
| PLATFORM.mgu74bv2 | Constant Option |
| PLATFORM.mgu74c | Constant Option |
| PLATFORM.mgu74cv2 | Constant Option |
| PLATFORM.mgug4104a | Constant Option |
| PLATFORM.mgug4120a | Constant Option |
| PLATFORM.mgug4121a | Constant Option |
| PLATFORM.mgug4122a | Constant Option |
| PLATFORM.moe430a | Constant Option |
| PLATFORM.moe430b | Constant Option |
| PLATFORM.MouseWG.6.v1.0.Bead.Array | Constant Option |
| PLATFORM.MouseWG.6.v2.0.Bead.Array | Constant Option |
| PLATFORM.rat2302 | Constant Option |
| PLATFORM.Rat.v1.0.Bead.Array | Constant Option |
| PLATFORM.rgu34a | Constant Option |
| PLATFORM.rgu34b | Constant Option |
| PLATFORM.rgu34c | Constant Option |
| PLATFORM.rgug4105a | Constant Option |
| PLATFORM.rgug4130a | Constant Option |
| PLATFORM.rgug4131a | Constant Option |
| PoolReplicate | Pool the replicated gene symbols |
| PoolReplicate-matrix-method | Title Handle Duplicated Gene Symbol |
| PoolReplicate-Study-method | Title Handle Duplicated Gene Symbol |
| print.Study | Title Custom print Function |
| ReadClinical | Title Read Clinical File |
| ReadExpr | Import and reformat gene expression data set |
| REPLICATE.all | Constant Option |
| REPLICATE.average | Constant Option |
| REPLICATE.IQR | Constant Option |
| REPLICATE.largest | Constant Option |
| setClinical | Title Set Clinical Data |
| show-Study-method | Title Custom show Function |
| SPECIES.all | Constant Option |
| SPECIES.entrez.all | Constant Option |
| SPECIES.entrez.human | Constant Option |
| SPECIES.entrez.mouse | Constant Option |
| SPECIES.entrez.rat | Constant Option |
| SPECIES.human | Constant Option |
| SPECIES.mouse | Constant Option |
| SPECIES.rat | Constant Option |
| SPECIES.refseq.all | Constant Option |
| SPECIES.refseq.human | Constant Option |
| SPECIES.refseq.mouse | Constant Option |
| SPECIES.refseq.rat | Constant Option |
| Study-class | Title Study Class |
| study.eg | An Study object with clinical data |
| stype | Title Generic Function: stype |
| STYPE.all | Constant Option |
| stype-methods | stype method |
| STYPE.multiple | Constant Option |
| STYPE.single | Constant Option |
| to.matrix | Title Study to matrix |
| TO.MATRIX.clinicals | Constant Option |
| TO.MATRIX.datasets | Constant Option |
