Man pages for bedapub/ribiosExpression
Expression Analysis with RibiosExpression
| annotate | Annotate eSet or probesets |
| assertFullRank | Assert whether a matrix is of full rank numerically |
| contrastAnnotation | Extract the contrast annotation data.frame from an object |
| contrastAnnotation-set | Assign contrast annotaiton to an object |
| contrastMatrix | Extract the contrast matrix from an object |
| contrastMatrix-set | Assign contrast matrix to an object |
| contrastNames | Extract contrastNames from an object |
| contrastSampleIndices | Return indices of samples involved in the given contrast of... |
| dataFrameTwoVecs | Build a data.frame from two vectors of potential different... |
| design2group | Infer groups from a design matrix |
| DesignContrast | Contrast a DesignContrast object |
| DesignContrast-class | Study design and contrast information |
| designMatrix | Extract the design matrix from an object |
| designMatrix-set | Assign design matrix to an object |
| designVariables | Extract design variable names from an object |
| dispGroups | Extract displayed group labels from an object |
| eSetToLongTable | Transform eSet to long data.frame |
| exprsToLong | Transform an expression matrix to long table |
| fixDesignMatrixColnames | Fix design matrix colnames so that they are legal variable... |
| fixEmptyColumnName | Detect if any column has an empty string as name and fix |
| formatGmt | Make strings in the GMT format |
| groups | Extract sample groups from an object |
| grp2gmt | Convert GRP files into GMT-formatted strings |
| isInputDesignConsistent | Test whether the input design matrix is consistent with the... |
| keepMaxStatProbe | Filter multiple probesets matching to the same gene by... |
| limmaDgeTable | Return dgeTable from a marrayLM object |
| limmaTopTable2dgeTable | Transform limma::topTable results to a DGEtable |
| matrixToLongTable | Transform a matrix to long table |
| mergeEset | Merge two eSets by column binding |
| nContrast | Extract the number of contrasts from an object |
| parseContrastStr | Parse contrast from strings |
| parseDesignContrast | Parse study design and asked questions encoded in design and... |
| parseDesignContrastFile | Parse design and contrast from files |
| parseDesignContrastStr | Parse design and contrast from strings |
| plot.DesignContrast | Plot a DesignContrast object with two heatmaps |
| readAnnotationFile | Read in an annotation file in the tsv-format, with or without... |
| readEset | Read eSet object from plain files |
| readExprsMatrix | Read an expression matrix into an ExpressionSet object |
| readFeatureAnnotationFile | Read in feature annotation file in the tsv-format, with or... |
| readFKtable | Read table with Foreign Keys |
| readGctCls | Import ExpressionSet into gct/cls files the C version, about... |
| readSampleAnnotationFile | Read in sample annotation file in the tsv-format, with or... |
| reannotate | Transform an eSet object of Bioc-annotation into of... |
| removeAllZeroVar | Remove all-zero variables from design matrix and the... |
| removeColRank | Return rank of the matrix and the ranks of resulting matrices... |
| ribiosExpression-package | Data structures and functions for gene expression analysis |
| ribiosExpressionSet | ribiosExpressionSet: An example of ExpressionSet with... |
| ribios.ExpressionSet | An ExpressionSet for case demonstrations |
| rowscale.ExpressionSet | Perform row-wise scaling to an ExpressionSet object |
| sniffFeatureType | Sniff the feature type of an object that implements the... |
| splitPCA | Split an eSet object and run PCA on each split, return PCA... |
| summarizeProbesets | Summarize probesets belonging to the same gene |
| summarizeSamples | Summarize samples by applying the function to sample subsets |
| truncateDgeTable | Truncate dgeTable into tables of positively and negatively... |
| writeEset | Export an ExpressionSet object as tab-delimited (or gct)... |
| writeGct | Export matrix or eEset that can be coereced as one into... |
| writeGctCls | Export ExpressionSet as Gct/Cls files |
| writeSampleGroups | Write sample groups and group levels into plain text files |
| writeVarMetadata | writexlxs: write AnnotatedDataFrame to a xlsx file |
