| Annotate an EdgeObject | annotate,EdgeObject,character,logical-method |
| Annotate an EdgeObject, without checking the target | annotate,EdgeObject,character,missing-method |
| Annotate an EdgeObject automatically without checking the target | annotate,EdgeObject,missing,missing-method |
| Get annotation information from an EdgeObject | annotation,EdgeObject-method |
| Append degree of freedom and pseudo t-statistics to dgeTable | appendPseudoT |
| Append ranks to dgeTbl | appendRanks |
| Append zscores to dgeTable | appendZScore |
| Assert that the input data.frame is a valid EdgeTopTable | assertEdgeToptable |
| Get aveExpr threshold in LimmaSigFilter | aveExpr |
| Return a data.frame of BCV values | BCV BCV,DGEList-method BCV,EdgeResult-method |
| Boxplot of an EdgeObject | boxplot,EdgeObject-method |
| Calculate normalisation factor if not | calcNormFactorsIfNot |
| Check sample annotation data.frame or tibble meets the requirement of the biokit pipeline | checkBiokitSampleAnnotation |
| Check a contrast matrix to make sure that it is likely o.k. | checkContrastNames |
| Common biological coefficients of variance (BCV) | commonBCV commonBCV,DGEList-method commonBCV,EdgeResult-method |
| Common dispersion | commonDisp commonDisp,DGEList-method commonDisp,EdgeObject-method |
| commonDisp-set | commonDisp<- commonDisp<-,DGEList,numeric-method commonDisp<-,EdgeObject,numeric-method |
| Assign contrast matrix | contrastMatrix-set contrastMatrix<- contrastMatrix<-,EdgeObject,matrix-method |
| Extract contrast matrix from an EdgeObject object | contrastMatrix,EdgeObject-method |
| Extract contrast matrix from an EdgeResult object | contrastMatrix,EdgeResult-method |
| Extract contrast names from an EdgeObject object | contrastNames,EdgeObject-method |
| Extract contrast names from an EdgeResult object | contrastNames,EdgeResult-method |
| Extract contrast sample indices | contrastSampleIndices,EdgeResult,character-method |
| Extract contrast sample indices | contrastSampleIndices,EdgeResult,integer-method |
| Sample counts by group | countByGroup hasNoReplicate maxCountByGroup |
| Object that contains count data, dgeTables, and sigFilter | CountDgeResult-class |
| Return counts in a DGEList object | counts,DGEList-method |
| Return counts in EdgeObject | counts,EdgeObject-method |
| Apply SVA to transformed count data and return the transformed matrix removing the effect of surrogate variables | countsRemoveSV |
| Apply SVA to transformed count data | countsSVA |
| cpm for EdgeObject | cpm.EdgeObject |
| Filter by counts per million (cpm) | cpmFilter |
| Apply cpm to voom-transformed count data, and return the voom expression matrix with surrogate variables' effect removed | cpmRemoveSV |
| Apply SVA to cpm-transformed count data | cpmSVA |
| Custom smear plot | customSmearPlot |
| Retrieve the design/contrast object | designContrast |
| Assign the design matrix | designMatrix-set designMatrix<- designMatrix<-,EdgeObject,matrix-method |
| Extract design matrix from an EdgeObject object | designMatrix,EdgeObject-method |
| Extract design matrix from an EdgeResult object | designMatrix,EdgeResult-method |
| Return the dgeGML method | dgeGML |
| Extract DGEList from an EdgeObject | dgeList dgeList,EdgeObject-method dgeList,EdgeResult-method |
| Construct a DGEListList object | DGEListList |
| An S4 class to represent a list of DGEListList objects | DGEListList-class |
| Convert a DGEList object to a long data.frame containing expression, feature annotation, and sample annotation | DGEListToLongTable |
| Return the top table in a unified format | dgeTable |
| Return the top tables of specified contrast(s) in a list | dgeTableList |
| Return a list of differential gene expression tables | dgeTables |
| Append dgeTables with pseudo t-statistic | dgeTablesWithPseudoT |
| Append dgeTables with z-scores | dgeTablesWithZScore |
| Append dgeTable with pseudo t-statistic | dgeTableWithPseudoT |
| Append dgeTable with z-scores | dgeTableWithZScore |
| Perform differential gene expression analysis with edgeR | dgeWithEdgeR |
| Perform differential gene expression analysis with edgeR-limma | dgeWithLimmaVoom |
| Dimensions of an EdgeResults | dim.EdgeResult |
| Get display labels of sample groups | dispGroups,EdgeObject-method |
| Perform surrogate variable analysis (SVA) to an EdgeObject object | doSVA |
| Construct an EdgeObject object by a count matrix and DesignContrast | EdgeObject |
| EdgeObject argumenting DGEList by including designContrast information | EdgeObject,DGEList,DesignContrast-method EdgeObject,FeatAnnoExprs,DesignContrast-method EdgeObject,matrix,DesignContrast-method EdgeObject-class |
| Export an DGEList, designMatrix, and contrastMatrix to files and return the command to run the edgeR script | edgeRcommand |
| Return a list of differential gene expression tables | EdgeResult |
| Object that contains test results, dgeTable, and SigFilter | EdgeResult-class |
| Extends BaseSigFilter to filter genes base on logCPM and LR | EdgeSigFilter-class |
| Transform an EexpressionSet to a DGEList object | eset2DGEList |
| Return an example of EdgeObject | exampleEdgeObject |
| Export dgeTest results | exportEdgeResult |
| Export static gene-level plots in PDF | exportStaticGeneLevelPlots |
| Get fData | fData,DGEList-method |
| Get fData | fData,EdgeObject-method |
| Set fData | fData<-,DGEList,data.frame-method |
| Set fData | fData<-,EdgeObject,data.frame-method |
| A class that contain feature annotation and expression matrix | FeatAnnoExprs-class |
| Feature names | featureNames,EdgeObject-method |
| Filter lowly expressed genes by counts per million (CPM) | filterByCPM |
| Filter lowly expressed genes by CPM in DGEList | filterByCPM.DGEList |
| Filter EdgeObj and remove lowly expressed genes | filterByCPM.EdgeObject |
| Filter lowly expressed genes by CPM | filterByCPM.matrix |
| Fit generalized linear model | fitGLM fitGLM,EdgeObject-method |
| Get GCT filename from a directory | gctFilename |
| Return gene count | geneCount |
| Return gene identifier types | geneIdentifierTypes |
| Get automatic group color | groupCol |
| Get sample groups from an EdgeObject object | groups,EdgeObject-method |
| Print a kdTable nicely with gt | gtKdTable |
| Tells whether common dispersion has been set | hasCommonDisp hasCommonDisp,DGEList-method hasCommonDisp,EdgeObject-method |
| Get human gene symbols for gene-set enrichment analysis | humanGeneSymbols humanGeneSymbols,DGEList-method humanGeneSymbols,EdgeObject-method |
| Infer surrogate variables | inferSV inferSV,DGEList,formula-method inferSV,DGEList,matrix-method inferSV,matrix,matrix-method |
| Is the object annotated | isAnnotated isAnnotated,EdgeObject-method |
| Is the Surrogate Variable (SV) matrix empty | isEmptySV |
| Return logical vector indicating which genes are significantly regulated | isSig isSigNeg isSigPos |
| Whether the aveExpr filter is set | isUnsetAveExpr |
| Whether the logCPM filter is set | isUnsetLogCPM |
| Tells whether the threshold was not set | isUnsetFDR isUnsetNegLogFC isUnsetPosLogFC isUnsetPValue |
| Whether the SigFilter is the default one | isUnsetSigFilter |
| Retrieve a knockdown table from edgeRes | kdTable |
| LimmaSigFilter Extending BaseSigFilter to filter genes base on aveExpr | LimmaSigFilter-class |
| Construct a LimmaVoomResult object | LimmaVoomResult |
| The LimmaVoom Object that contains test results, dgeTable, and SigFilter | LimmaVoomResult-class |
| Get settings in the EdgeSigFilter | logCPM |
| Extract a matrix of log2(fold-change) values | logFCmatrix |
| Perform principal component analysis to the log fold-change matrix | logFCmatrixPCA |
| Perform principal component analysis to an EdgeResult object | logFCpca |
| Send an edgeR analysis job to SLF | lsfEdgeR |
| Return the LSF command to run the edgeR script | lsfEdgeRcommand |
| Merge two DGEList objects into one | mergeDGEList |
| Return the size of the smallest group | minGroupCount minGroupCount.DGEList minGroupCount.EdgeObject |
| Build design matrix from a DGEList object | model.DGEList |
| Modulated logCPM | modLogCPM modLogCPM,DGEList-method modLogCPM,EdgeObject-method |
| Return either NA (if input is NULL) or sqrt | naOrSqrt |
| Return number of samples | ncol,EdgeResult-method |
| Return the number of contrasts | nContrast,EdgeResult-method |
| Normalize an EdgeObject | normalize,EdgeObject-method |
| Plot distribution of normalized counts | normBoxplot |
| Extract normalisation factors from the object | normFactors normFactors,DGEList-method normFactors,EdgeObject-method |
| Return number of features | nrow,EdgeResult-method |
| Pairs plot for EdgeResult | pairs.EdgeResult |
| Parse feature information from molecular-phenotyping GCT files | parseMolPhenFeat |
| Get pData (sample annotation) | pData,DGEList-method |
| Get pData | pData,EdgeObject-method |
| Set pData (sample annotation) | pData<-,DGEList,data.frame-method |
| Set pData (sample annotation) | pData<-,EdgeObject,data.frame-method |
| Plot BCV | plotBCV plotBCV,DGEList-method plotBCV,EdgeObject-method plotBCV,EdgeResult-method |
| Plot gene expression with knockdown efficiency | plotKnockdown |
| plotMDS for EdgeObject | plotMDS.EdgeObject |
| Plot top significantly differentially expressed genes by contrast | plotTopSigGenes |
| Plot top significantly differentially expressed genes by contrast | plotTopSigGenesByContrast |
| Get settings in the significance filter | FDR negLogFC posLogFC pValue |
| Update SigFilter | aveExpr<- FDR<- logCPM<- logFC<- negLogFC<- posLogFC<- pValue<- update.EdgeSigFilter update.LimmaSigFilter update.SigFilter `aveExpr<-` `FDR<-` `logCPM<-` `logFC<-` `negLogFC<-` `posLogFC<-` `pValue<-` |
| Principal component analysis of DGEList | prcomp.DGEList |
| Run principal component analysis on a DGEListList object | prcomp.DGEListList |
| Principal component analysis of an expression matrix | prcompExprs |
| Convert p-values to t-statistics | pseudoTfromPvalue |
| Return a range determined by the quantile of the data | quantileRange |
| Read Illumina MolPhen sample sheet from XLS files | read_illumina_sampleSheet_xls |
| Read a Biokit output directory into a DGEList object for downstream analysis | readBiokitAsDGEList |
| Read feature annotation from Biokit directory | readBiokitFeatureAnnotation |
| Read GCT files from Biokit output directory | readBiokitGctFile |
| Read Biokit phenodata | readBiokitPhenodata |
| Read feature annotation for EdgeR pipeline | readFeatureAnnotationForEdgeR |
| Read molecular phenotyping output folder into a DGEList object | readMolPhenAsDGEList |
| Read molecular phenotyping coverage file | readMolPhenCoverageGct |
| Read mpsnake output directory into a DGEList object | readMpsnakeAsDGEList |
| Read sample annotation from tab-delimited file for EdgeR analysis | readSampleAnnotationForEdgeR |
| Rename contrast by a pair of vectors | renameContrast |
| Rename contrast by a function | renameContrastByFunc |
| Replace NA counts with zero counts | replaceNAwithZero |
| _PACKAGE | ribiosNGS |
| Variance of features in rows | rowVars |
| Convert a RPKM matrix to a TPM matrix | rpkm2tpm |
| Return sample names from a DGEList object | sampleNames,DGEList-method |
| Sample names | sampleNames,EdgeObject-method |
| Set common dispersion if missing | setCommonDispIfMissing setCommonDispIfMissing,DGEList,numeric-method setCommonDispIfMissing,EdgeObject,numeric-method |
| Show DGEList | show,DGEList-method |
| Show DGEListList | show,DGEListList-method |
| Show an EdgeResult object | show,EdgeResult-method |
| Show an EdgeSigFilter object | show,EdgeSigFilter-method |
| Show an LimmaSigFilter object | show,LimmaSigFilter-method |
| Show an SigFilter object | show,SigFilter-method |
| Retrieve SigFilter objects from other objects Return the SigFilter in use | sigFilter |
| Build a SigFilter | EdgeSigFilter LimmaSigFilter SigFilter |
| Base result filter for significantly regulated genes | SigFilter-class |
| Replace the SigFilter of an CountDgeResult | sigFilter<- |
| Return significantly regulated genes | sigGene sigNegGene sigPosGene |
| Barchart of significantly regulated genes | sigGeneBarchart |
| Return counts of significantly regulated genes | sigGeneCounts |
| Return dgeTable containing significantly regulated genes in respective contrasts | sigGeneDgeTable |
| Return gene identifiers of significant DGEs | sigGeneIdentifiers |
| Return significantly regulated genes of all contrasts | sigGenes sigNegGenes sigPosGenes |
| Send an edgeR analysis job to SLURM | slurmEdgeR |
| Return the SLURM command to run the edgeR script | slurmEdgeRcommand |
| Smear plot | smearPlot smearPlot,EdgeResult-method |
| Split a DGEList object by a factor of samples (default) or genes | split.DGEList splitDGEList |
| Make static gene-level plots of an EdgeResult object | staticGeneLevelPlots |
| Detect surrogate variables from count data and remove their effects VSN-transformed counts | svaseqRemove |
| Tagwise biological coefficients of variance | tagwiseBCV tagwiseBCV,DGEList-method tagwiseBCV,EdgeResult-method |
| Test GLM | testGLM testGLM,EdgeObject,DGEGLM-method |
| Return raw expression of top differentially expressed genes of multiple contrasts | topDgeExpression |
| Return raw expression of top differentially expressed genes of one contrast | topDgeExpressionByContrast |
| Convert count matrix to TPM values | tpm |
| Trended biological coefficients of variance | trendedBCV trendedBCV,DGEList-method trendedBCV,EdgeResult-method |
| Update a contrast matrix given a surrogate variable matrix | updateContrastMatrixWithSV |
| Update design matrix by SVA | updateDesignMatrixBySVA updateDesignMatrixBySVA,DGEList,formula-method |
| Update the SigFilter | updateSigFilter |
| Volcano plot | volcanoPlot volcanoPlot,EdgeResult-method |
| Perform VOOM analysis | voom voom,DGEList-method voom,EdgeObject-method voom,ExpressionSet-method voom,matrix-method |
| Perform the voom+limma procedure | voomLimma |
| Apply SVA to voom-transformed count data, and return the voom expression matrix with surrogate variables' effect removed | voomRemoveSV |
| Run SVA on a count matrix transformed by voom | voomSVA voomSVA,DGEList,formula-method voomSVA,DGEList,matrix-method voomSVA,matrix,matrix-method |
| Write sample annotation into a tab-delimited file to start the Biokit pipeline | writeBiokitSampleAnnotation |
| Write an DGEList object as plain files for downstream analysis | writeDGEList |
| Write DGE tables in individual files, and the merged table in one file | writeDgeTables |
| Write dgeTables with pseudo T statistics | writeDgeTablesWithPseudoT |
| Write truncated DGE tables | writeTruncatedDgeTables |
