Man pages for pathwayPCA
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
| aespca | Adaptive, elastic-net, sparse principal component analysis |
| AESPCA_pVals | Test pathway association with AES-PCA |
| CheckAssay | Check an Input Assay |
| CheckPwyColl | Check an Input Pathway Collection |
| CheckSampleIDs | Check Input Sample IDs |
| colon_pathwayCollection | Gene Pathway Subset |
| colonSurv_df | Colon Cancer -Omics Data |
| Contains | Check if a long atomic vector contains a short atomic vector |
| ControlFDR | Adjust p-values for simple multiple-testing procedures |
| coxTrain_fun | Train Cox Proportional Hazards model for supervised PCA |
| CreateOmics | Generation Wrapper function for '-Omics*'-class objects |
| CreateOmicsPathway | Generation functions for '-Omics*'-class objects |
| CreatePathwayCollection | Manually Create a 'pathwayCollection'-class Object. |
| ExtractAESPCs | Extract AES-PCs from recorded pathway-subsets of a mass... |
| getPathPCLs | Extract PCs and Loadings from a 'superpcOut'- or... |
| getPathpVals | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'-... |
| get_set_OmicsPathway | Access and Edit Assay or 'pathwayCollection' Values in... |
| get_set_OmicsRegCateg | Access and Edit Response of an 'OmicsReg' or 'OmicsReg'... |
| get_set_OmicsSurv | Access and Edit Event Time or Indicator in an 'OmicsSurv'... |
| glmTrain_fun | Gene-specific Generalized Linear Model fit statistics for... |
| GumbelMixpValues | Calculate the p-values from an optimal mixture of Weibull... |
| IntersectOmicsPwyCollct | Delete -Ome symbols or IDs without matching features recorded... |
| JoinPhenoAssay | Merge Phenotype and Assay Data by First Column (Sample ID) |
| lars.lsa | Least Angle Regression and LASSO Regression |
| LoadOntoPCs | Calculate Test Data PCs from Training-Data Estimated Loadings |
| mysvd | Singular Value Decomposition wrapper for supervised PCA |
| normalize | Normalize and reconstruct the eigenvalues of a data matrix... |
| olsTrain_fun | Gene-specific Regularized Ordinary Least Squares fit... |
| OmicsCateg-class | An S4 class for categorical responses within an... |
| OmicsPathway-class | An S4 class for mass spectrometry or bio-assay data and gene... |
| OmicsReg-class | An S4 class for continuous responses within an 'OmicsPathway'... |
| OmicsSurv-class | An S4 class for survival responses within an 'OmicsPathway'... |
| OptimGumbelMixParams | Calculate the optimal parameters for a mixture of Weibull... |
| pathwayPCA-package | Extract and Test the Significance of Pathway-Specific... |
| pathway_tControl | Calculate pathway-specific Student's t-scores from a null... |
| pathway_tScores | Calculate pathway-specific Student's t-scores for supervised... |
| PathwaytValues | Calculate pathway-specific Student's t-scores from a null... |
| PermTestCateg | AES-PCA permutation test of categorical response for pathway... |
| PermTestReg | AES-PCA permutation test of continuous response for pathway... |
| PermTestSurv | AES-PCA permutation test of survival response for pathway PCs |
| permuteSamps | Parametric bootstrap and non-parametric permutations of a... |
| print.pathwayCollection | Display the Summary of a 'pathwayCollection'-class Object. |
| read_gmt | Read a '.gmt' file in as a 'pathwayCollection' object |
| SE2Tidy | Tidy a SummarizedExperiment Assay |
| show-OmicsPathway-method | Display the Summary of an 'Omics*'-class Object. |
| SubsetPathwayCollection | Subset a 'pathwayCollection'-class Object by Pathway. |
| SubsetPathwayData | Subset Pathway-Specific Data |
| SuperPCA_pVals | Test pathways with Supervised PCA |
| superpc.st | Extract and test principal components from supervised PCA |
| superpc.train | Train a supervised PCA model |
| TabulatepValues | Tabulate, adjust, and sort pathway p-values |
| TransposeAssay | Transpose an Assay (Data Frame) |
| ValidOmicsSurv | Check validity of new Omics*-class objects |
| WhichPathways | Filter and Subset a 'pathwayCollection'-class Object by... |
| wikipwsHS_Entrez_pathwayCollection | Wikipathways Homosapiens EntrezIDs |
| wikipwsHS_Symbol_pathwayCollection | Wikipathways Homosapiens Gene Symbols |
| write_gmt | Write a 'pathwayCollection' Object to a '.gmt' File |
