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 |

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... |

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... |

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 |

show-OmicsPathway-method | Display the Summary of an 'Omics*'-class Object. |

SubsetPathwayCollection | Subset a 'pathwayCollection'-class Object. |

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 |

wikipwsHS_Entrez_pathwayCollection | Wikipathways Homosapiens EntrezIDs |

write_gmt | Write a 'pathwayCollection' Object to a '.gmt' File |

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