Man pages for aiminy/PathwaySJ
A R package for GO term enrichment analysis with the flexible bias factor adjustment
| callQoRT | Use QoRTs to get the count of subfeatures in each gene |
| Combine3Re | Combine3Re |
| CombineCpTftGoGeneID | CombineCpTftGoGeneID |
| CompareDEfromGeneWithDEfromFeatures | CompareDEfromGeneWithDEfromFeatures |
| CompareGOResults | CompareGOResults |
| Draw4Cat | Draw4Cat |
| Draw4GO | Draw4GO |
| DrawFeature | DrawFeature |
| ExtractGeneIDFromGo | ExtractGeneIDFromGo |
| FDR_genewise | Title |
| gene2cat | gene2cat |
| gene2cat2 | gene2cat2 |
| GeneBasedAnalysis | GeneBasedAnalysis |
| GenerateGeneAnno | Generate gene annotations based on the Ensembl ID of genes |
| GeneWisePvsExonWiseP | Compare gene based p value with exon based p value |
| GetCCBetweenMostSigPadjustSJ | Title |
| getDataset | codes for simulation and plot PWF simulation code from... |
| GetDesign | Title |
| getgo | #############################################################################... |
| getgo3 | Title |
| GetMgiSymbolDescription | Title |
| GetMgiSymbolUsingLocalDataBase | Title |
| Get_Over_under_represented_pvalue | calculate the p-value for GO terms |
| GetPwfUseReformatedData | GetPwfUseReformatedData |
| GetResults4GeneLevel | GetResults4GeneLevel |
| GetResultsFromJunctionSeq | Get analysis results using JunctionSeq |
| Gmt2GeneCat | Gmt2GeneCat |
| goseq2 | goseq2 |
| GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene | This function is to subset data set based on feature |
| GotermAnalysisUseFeatureDefineDE | GotermAnalysisUseFeatureDefineDE |
| GotermAnalysisUseReformatedData | GotermAnalysisUseReformatedData |
| GSA.read.gmt.2 | GSA.read.gmt.2 |
| JS.perGeneQValue | JS.perGeneQValue |
| JS.perGeneQValueExact | JS.perGeneQValueExact |
| JS.perGeneQValueExact.test | Title |
| LabelGeneBasedFeature | LabelGeneBasedFeature |
| list_to_df | Title |
| makeGeneWiseTable | This function is to generate the gene-based results |
| NBsim | Generate simulated count based on NB distribution |
| OuputGO | OutputGO |
| OutputCatBasedPwf | OutputCatBasedPwf |
| OutputFigure | Title |
| OutputGeneWiseTable | Title |
| OutputGOBasedDEfromFeatures | OutputGOBasedDEfromFeatures |
| OutputGOBasedDEfromFeatures2 | OutputGOBasedDEfromFeatures2 |
| OutputGOBasedDEfromFeatures3 | OutputGOBasedDEfromFeatures3 |
| PermutattionOfRawData | Title |
| plotPWF2 | Plot the probability Weighting Function |
| ProcessCuffLinkResults | ProcessCuffLinkResults |
| ProcessOutputFilesFrom_rMATS | ProcessOutputFilesFrom_rMATS |
| readJunctionSeqCounts | Title |
| ReformatData | Title |
| ReformatDataUseTable | ReformatDataUseTable |
| reversemapping | Title |
| Select_DE_gene_basd_on_Feature | Select_DE_gene_based_on_Feature |
| SelectFeature | SelectFeature |
| SimulationSJ2DE | Simulate gene sets based on the number of splicing junctions |
| UseLogistic2_adDE | Title |
| UseLogistic2CKBias | Title |
| UseOtherDataSet | Title |
