Package: pathwayPCA
Type: Package
Title: Integrative Pathway Analysis with Modern PCA Methodology and
        Gene Selection
Version: 1.0.0
Authors@R: c(person("Gabriel", "Odom", email = "gabriel.odom@med.miami.edu", role = c("aut","cre")),
  person("James", "Ban", email = "yuguang.ban@med.miami.edu", role = c("aut")),
  person("Lizhong", "Liu", email = "lxl816@miami.edu", role = c("aut")),
  person("Lily", "Wang", email = "lily.wang@med.miami.edu", role = c("aut")),
  person("Steven", "Chen", email = "steven.chen@med.miami.edu", role = c("aut")))
Description: Apply the Supervised PCA and Adaptive, Elastic-Net, Sparse PCA
  methods to extract principal components from each pathway. Use these pathway-
  specific principal components as the design matrix relating the response to
  each pathway. Return the model fit statistic p-values, and adjust these values
  for False Discovery Rate. Return a data frame of the pathways sorted by their
  adjusted p-values. This package has corresponding vignettes hosted in the
  ''User Guides'' page of <https://gabrielodom.github.io/pathwayPCA/index.html>,
  and the website for the development information is hosted at
  <https://github.com/gabrielodom/pathwayPCA>.
License: GPL-3
Depends: R (>= 3.6)
Imports: lars, methods, parallel, stats, survival, utils
Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2,
        rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
biocViews: CopyNumberVariation, DNAMethylation, GeneExpression, SNP,
        Transcription, GenePrediction, GeneSetEnrichment,
        GeneSignaling, GeneTarget, GenomeWideAssociation,
        GenomicVariation, CellBiology, Epigenetics, FunctionalGenomics,
        Genetics, Lipidomics, Metabolomics, Proteomics, SystemsBiology,
        Transcriptomics, Classification, DimensionReduction,
        FeatureExtraction, PrincipalComponent, Regression, Survival,
        MultipleComparison, Pathways
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Collate: 'CreatePathwayCollection.R' 'createClass_OmicsPath.R'
        'createClass_validOmics.R' 'accessClass_OmicsPath.R'
        'createClass_OmicsSurv.R' 'accessClass_OmicsSurv.R'
        'accessClass_OmicsRegCateg.R' 'createClass_OmicsCateg.R'
        'createClass_OmicsReg.R' 'accessClass_OmicsPathData.R'
        'accessClass_pathwayCollection.R' 'accessClass_pcOut.R'
        'accessClass_pcOutpVals.R' 'aesPC_calculate_AESPCA.R'
        'aesPC_calculate_LARS.R' 'aesPC_extract_OmicsPath_PCs.R'
        'aesPC_permtest_CoxPH.R' 'aesPC_permtest_GLM.R'
        'aesPC_permtest_LM.R' 'aesPC_unknown_matrixNorm.R'
        'aesPC_wrapper.R' 'createOmics_All.R'
        'createOmics_CheckAssay.R'
        'createOmics_CheckPathwayCollection.R'
        'createOmics_CheckSampleIDs.R' 'createOmics_JoinPhenoAssay.R'
        'createOmics_TrimPathwayCollection.R' 'createOmics_Wrapper.R'
        'data_colonSubset.R' 'data_genesetSubset.R'
        'data_wikipathways.R' 'pathwayPCA.R' 'printClass_Omics_All.R'
        'printClass_pathwayCollection.R' 'superPC_model_CoxPH.R'
        'superPC_model_GLM.R' 'superPC_model_LS.R'
        'superPC_model_tStats.R' 'superPC_model_train.R'
        'superPC_modifiedSVD.R' 'superPC_optimWeibullParams.R'
        'superPC_optimWeibull_pValues.R' 'superPC_pathway_tControl.R'
        'superPC_pathway_tScores.R' 'superPC_pathway_tValues.R'
        'superPC_permuteSamples.R' 'superPC_wrapper.R'
        'utils_adjust_and_sort_pValues.R'
        'utils_load_test_data_onto_PCs.R' 'utils_multtest_pvalues.R'
        'utils_read_gmt.R' 'utils_stdExpr_2_tidyAssay.R'
        'utils_transpose_assay.R' 'utils_write_gmt.R'
VignetteBuilder: knitr
URL: https://gabrielodom.github.io/pathwayPCA/;
        https://github.com/gabrielodom/pathwayPCA
BugReports: https://github.com/gabrielodom/pathwayPCA/issues
git_url: https://git.bioconductor.org/packages/pathwayPCA
git_branch: RELEASE_3_9
git_last_commit: 670c10f
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
NeedsCompilation: no
Packaged: 2019-05-03 05:46:11 UTC; biocbuild
Author: Gabriel Odom [aut, cre],
  James Ban [aut],
  Lizhong Liu [aut],
  Lily Wang [aut],
  Steven Chen [aut]
Maintainer: Gabriel Odom <gabriel.odom@med.miami.edu>
Built: R 3.6.0; ; 2019-05-03 14:05:47 UTC; windows
