Man pages for gabrielodom/pathwayPCA
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

aespcaAdaptive, elastic-net, sparse principal component analysis
AESPCA_pValsTest pathway association with AES-PCA
CheckAssayCheck an Input Assay
CheckPwyCollCheck an Input Pathway Collection
CheckSampleIDsCheck Input Sample IDs
colon_pathwayCollectionGene Pathway Subset
colonSurv_dfColon Cancer -Omics Data
ControlFDRAdjust p-values for simple multiple-testing procedures
coxTrain_funTrain Cox Proportional Hazards model for supervised PCA
CreateOmicsGeneration Wrapper function for '-Omics*'-class objects
CreateOmicsPathwayGeneration functions for '-Omics*'-class objects
CreatePathwayCollectionManually Create a 'pathwayCollection'-class Object.
ExtractAESPCsExtract AES-PCs from recorded pathway-subsets of a mass...
getPathPCLsExtract PCs and Loadings from a 'superpcOut'- or...
get_set_OmicsPathwayAccess and Edit Assay or 'pathwayCollection' Values in...
get_set_OmicsRegCategAccess and Edit Response of an 'OmicsReg' or 'OmicsReg'...
get_set_OmicsSurvAccess and Edit Event Time or Indicator in an 'OmicsSurv'...
glmTrain_funGene-specific Generalized Linear Model fit statistics for...
GumbelMixpValuesCalculate the p-values from an optimal mixture of Weibull...
IntersectOmicsPwyCollctDelete -Ome symbols or IDs without matching features recorded...
JoinPhenoAssayMerge Phenotype and Assay Data by First Column (Sample ID)
lars.lsaLeast Angle Regression and LASSO Regression
LoadOntoPCsCalculate Test Data PCs from Training-Data Estimated Loadings
mysvdSingular Value Decomposition wrapper for supervised PCA
normalizeNormalize and reconstruct the eigenvalues of a data matrix...
olsTrain_funGene-specific Regularized Ordinary Least Squares fit...
OmicsCateg-classAn S4 class for categorical responses within an...
OmicsPathway-classAn S4 class for mass spectrometry or bio-assay data and gene...
OmicsReg-classAn S4 class for continuous responses within an 'OmicsPathway'...
OmicsSurv-classAn S4 class for survival responses within an 'OmicsPathway'...
OptimGumbelMixParamsCalculate the optimal parameters for a mixture of Weibull...
pathwayPCA-packageExtract and Test the Significance of Pathway-Specific...
pathway_tControlCalculate pathway-specific Student's t-scores from a null...
pathway_tScoresCalculate pathway-specific Student's t-scores for supervised...
PermTestCategAES-PCA permutation test of categorical response for pathway...
PermTestRegAES-PCA permutation test of continuous response for pathway...
PermTestSurvAES-PCA permutation test of survival response for pathway PCs
permuteSampsParametric bootstrap and non-parametric permutations of a...
print.pathwayCollectionDisplay the Summary of a 'pathwayCollection'-class Object.
read_gmtRead a '.gmt' file in as a 'pathwayCollection' object
show-OmicsPathway-methodDisplay the Summary of an 'Omics*'-class Object.
SubsetPathwayCollectionSubset a 'pathwayCollection'-class Object.
SubsetPathwayDataSubset Pathway-Specific Data
SuperPCA_pValsTest pathways with Supervised PCA
superpc.stExtract and test principal components from supervised PCA
superpc.trainTrain a supervised PCA model
TabulatepValuesTabulate, adjust, and sort pathway p-values
TransposeAssayTranspose an Assay (Data Frame)
ValidOmicsSurvCheck validity of new Omics*-class objects
wikipwsHS_Entrez_pathwayCollectionWikipathways Homosapiens EntrezIDs
write_gmtWrite a 'pathwayCollection' Object to a '.gmt' File
gabrielodom/pathwayPCA documentation built on Jan. 10, 2019, 9:39 p.m.