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. |