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