Man pages for gabrielodom/pathwayPCA
Test Pathways for Statistically Significant Relationships

adjust_and_sortAdjust and sort pathway p-values
adjustRaw_pValsAdjust p-values for simple multiple-testing procedures
aespcaAdaptive, elastic-net, sparse principal component analysis
AESPCA_pValsTest pathway association with AES-PCA
colon_pathwaySetGene Pathway Subset
colonSurv_dfColon Cancer -Omics Data
coxTrain_funTrain Cox Proportional Hazards model for supervised PCA
create_OmicsGeneration Wrapper function for '-Omics*'-class objects
create_OmicsPathwayGeneration functions for '-Omics*'-class objects
create_pathwaySetManually Create a 'pathwaySet'-class Object.
expressedOmesExtract expressed -Omes matching a pathways list from an...
extract_aesPCsExtract AES-PCs from expressed pathway-subsets of a mass...
get_set_OmicsPathwayAccess and Edit Assay or 'pathwaySet' Values in 'Omics*'...
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...
lars.lsaLeast Angle Regression and LASSO Regression
matrixRootPositive root of a symmetric matrix
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'...
pathwayPCA-packageExtract and Test the Significance of Pathway-Specific...
pathway_pValuesCalculate the p-values from a mixture of Weibull Extreme...
pathway_tControlCalculate pathway-specific Student's t-scores from a null...
pathway_tScoresCalculate pathway-specific Student's t-scores for supervised...
permTest_OmicsCategAES-PCA permutation test of categorical response for pathway...
permTest_OmicsRegAES-PCA permutation test of continuous response for pathway...
permTest_OmicsSurvAES-PCA permutation test of survival response for pathway PCs
permuteSampsParametric bootstrap and non-parametric permutations of a...
print.pathwaySetDisplay the Summary of a 'pathwaySet'-class Object.
read_gmtRead a '.gmt' file in as a 'pathwaySet' object
show-OmicsPathway-methodDisplay the Summary of an 'Omics*'-class Object.
superPCA_pValsTest pathways with supervised PCA
superpc.stExtract and test principal components from supervised PCA
superpc.trainTrain a supervised PCA model
transpose_assayTranspose an Assay (Data Frame)
valid_OmicsSurvCheck validity of new Omics*-class objects
weibullMix_optimParamsCalculate the optimal parameters for a mixture of Weibull...
weibullMix_pValuesCalculate the p-values from an optimal mixture of Weibull...
gabrielodom/pathwayPCA documentation built on May 3, 2018, 4:22 a.m.