Integrative Pathway Analysis with Modern PCA Methodology and
Gene Selection
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Documentation for package ‘pathwayPCA’ version 1.22.0
Help Pages
| aespca | Adaptive, elastic-net, sparse principal component analysis |
| AESPCA_pVals | Test pathway association with AES-PCA |
| AESPCA_pVals-method | Test pathway association with AES-PCA |
| colonSurv_df | Colon Cancer -Omics Data |
| colon_pathwayCollection | Gene Pathway Subset |
| Contains | Check if a long atomic vector contains a short atomic vector |
| CreateOmics | Generation Wrapper function for '-Omics*'-class objects |
| CreateOmicsCateg | Generation functions for '-Omics*'-class objects |
| CreateOmicsPath | Generation functions for '-Omics*'-class objects |
| CreateOmicsReg | Generation functions for '-Omics*'-class objects |
| CreateOmicsSurv | Generation functions for '-Omics*'-class objects |
| CreatePathwayCollection | Manually Create a 'pathwayCollection'-class Object. |
| getAssay | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getAssay-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getAssay<- | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getAssay<--method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getEvent | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEvent-method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEvent<- | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEvent<--method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEventTime | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEventTime-method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEventTime<- | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getEventTime<--method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| getPathPCLs | Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object. |
| getPathPCLs.aespcOut | Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object. |
| getPathPCLs.superpcOut | Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object. |
| getPathpVals | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object. |
| getPathpVals.aespcOut | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object. |
| getPathpVals.superpcOut | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object. |
| getPathwayCollection | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getPathwayCollection-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getPathwayCollection<- | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getPathwayCollection<--method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getResponse | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object |
| getResponse-method | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object |
| getResponse<- | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object |
| getResponse<--method | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object |
| getSampleIDs | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getSampleIDs-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getSampleIDs<- | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getSampleIDs<--method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getTrimPathwayCollection | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| getTrimPathwayCollection-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| LoadOntoPCs | Calculate Test Data PCs from Training-Data Estimated Loadings |
| OmicsCateg-class | An S4 class for categorical responses within an 'OmicsPathway' object |
| OmicsPathway-class | An S4 class for mass spectrometry or bio-assay data and gene pathway lists |
| OmicsReg-class | An S4 class for continuous responses within an 'OmicsPathway' object |
| OmicsSurv-class | An S4 class for survival responses within an 'OmicsPathway' object |
| pathwayPCA | Extract and Test the Significance of Pathway-Specific Principal Components |
| read_gmt | Read a '.gmt' file in as a 'pathwayCollection' object |
| SE2Tidy | Tidy a SummarizedExperiment Assay |
| SubsetOmicsPath | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects |
| SubsetOmicsResponse | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object |
| SubsetOmicsSurv | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object |
| SubsetPathwayCollection | Subset a 'pathwayCollection'-class Object by Pathway. |
| SubsetPathwayData | Subset Pathway-Specific Data |
| SubsetPathwayData-method | Subset Pathway-Specific Data |
| SuperPCA_pVals | Test pathways with Supervised PCA |
| SuperPCA_pVals-method | Test pathways with Supervised PCA |
| TransposeAssay | Transpose an Assay (Data Frame) |
| WhichPathways | Filter and Subset a 'pathwayCollection'-class Object by Symbol. |
| wikipwsHS_Entrez_pathwayCollection | Wikipathways Homosapiens EntrezIDs |
| wikipwsHS_Symbol_pathwayCollection | Wikipathways Homosapiens Gene Symbols |
| write_gmt | Write a 'pathwayCollection' Object to a '.gmt' File |
| [[.pathwayCollection | Subset a 'pathwayCollection'-class Object by Pathway. |