{ "_id": "6a1ac1171d7bb097a09d7835", "Package": "pathwayPCA", "Type": "Package", "Title": "Integrative Pathway Analysis with Modern PCA Methodology and\nGene Selection", "Version": "1.29.0", "Authors@R": "c(person(\"Gabriel\", \"Odom\", email = \"gabriel.odom@med.miami.edu\", role = c(\"aut\",\"cre\")),\nperson(\"James\", \"Ban\", email = \"yuguang.ban@med.miami.edu\", role = c(\"aut\")),\nperson(\"Lizhong\", \"Liu\", email = \"lxl816@miami.edu\", role = c(\"aut\")),\nperson(\"Lily\", \"Wang\", email = \"lily.wang@med.miami.edu\", role = c(\"aut\")),\nperson(\"Steven\", \"Chen\", email = \"steven.chen@med.miami.edu\", role = c(\"aut\")))", "Description": "pathwayPCA is an integrative analysis tool that implements\nthe principal component analysis (PCA) based pathway analysis\napproaches described in Chen et al. (2008), Chen et al. (2010),\nand Chen (2011). pathwayPCA allows users to: (1) Test pathway\nassociation with binary, continuous, or survival phenotypes.\n(2) Extract relevant genes in the pathways using the SuperPCA\nand AES-PCA approaches. (3) Compute principal components (PCs)\nbased on the selected genes. These estimated latent variables\nrepresent pathway activities for individual subjects, which can\nthen be used to perform integrative pathway analysis, such as\nmulti-omics analysis. (4) Extract relevant genes that drive\npathway significance as well as data corresponding to these\nrelevant genes for additional in-depth analysis. (5) Perform\nanalyses with enhanced computational efficiency with parallel\ncomputing and enhanced data safety with S4-class data objects.\n(6) Analyze studies with complex experimental designs, with\nmultiple covariates, and with interaction effects, e.g.,\ntesting whether pathway association with clinical phenotype is\ndifferent between male and female subjects. Citations: Chen et\nal. (2008) ;\nChen et al. (2010) ; and\nChen (2011) .", "License": "GPL-3", "biocViews": "CopyNumberVariation, DNAMethylation, GeneExpression, SNP,\nTranscription, GenePrediction, GeneSetEnrichment,\nGeneSignaling, GeneTarget, GenomeWideAssociation,\nGenomicVariation, CellBiology, Epigenetics, FunctionalGenomics,\nGenetics, Lipidomics, Metabolomics, Proteomics, SystemsBiology,\nTranscriptomics, Classification, DimensionReduction,\nFeatureExtraction, PrincipalComponent, Regression, Survival,\nMultipleComparison, Pathways", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.2.3", "Collate": "'CreatePathwayCollection.R' 'createClass_OmicsPath.R'\n'createClass_validOmics.R' 'accessClass_OmicsPath.R'\n'createClass_OmicsSurv.R' 'accessClass_OmicsSurv.R'\n'accessClass_OmicsRegCateg.R' 'createClass_OmicsCateg.R'\n'createClass_OmicsReg.R' 'accessClass_OmicsPathData.R'\n'accessClass_pathwayCollection.R'\n'accessClass_pathwayCollection_which.R' 'accessClass_pcOut.R'\n'accessClass_pcOutpVals.R' 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], "fields": [], "table": true, "tojson": true }, { "name": "wikipwsHS_Symbol_pathwayCollection", "title": "Wikipathways Homosapiens Gene Symbols", "object": "wikipwsHS_Symbol_pathwayCollection", "file": "wikipwsHS_Symbol_pathwayCollection.rda", "class": [ "pathwayCollection", "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "aespca", "title": "Adaptive, elastic-net, sparse principal component analysis", "topics": [ "aespca" ] }, { "page": "AESPCA_pVals", "title": "Test pathway association with AES-PCA", "topics": [ "AESPCA_pVals", "AESPCA_pVals,OmicsPathway-method" ] }, { "page": "colon_pathwayCollection", "title": "Gene Pathway Subset", "topics": [ "colon_pathwayCollection" ] }, { "page": "colonSurv_df", "title": "Colon Cancer -Omics Data", "topics": [ "colonSurv_df" ] }, { "page": "Contains", "title": "Check if a long atomic vector contains a short atomic vector", "topics": [ "Contains" ] }, { "page": "CreateOmics", "title": "Generation Wrapper function for '-Omics*'-class objects", "topics": [ "CreateOmics" ] }, { "page": "CreateOmicsPathway", "title": "Generation functions for '-Omics*'-class objects", "topics": [ "CreateOmicsCateg", "CreateOmicsPath", "CreateOmicsReg", "CreateOmicsSurv" ] }, { "page": "CreatePathwayCollection", "title": "Manually Create a 'pathwayCollection'-class Object.", "topics": [ "CreatePathwayCollection" ] }, { "page": "getPathPCLs", "title": "Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object.", "topics": [ "getPathPCLs", "getPathPCLs.aespcOut", "getPathPCLs.superpcOut" ] }, { "page": "getPathpVals", "title": "Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object.", "topics": [ "getPathpVals", "getPathpVals.aespcOut", "getPathpVals.superpcOut" ] }, { "page": "LoadOntoPCs", "title": "Calculate Test Data PCs from Training-Data Estimated Loadings", "topics": [ "LoadOntoPCs" ] }, { "page": "OmicsCateg-class", "title": "An S4 class for categorical responses within an 'OmicsPathway' object", "topics": [ "OmicsCateg-class" ] }, { "page": "OmicsPathway-class", "title": "An S4 class for mass spectrometry or bio-assay data and gene pathway lists", "topics": [ "OmicsPathway-class" ] }, { "page": "OmicsReg-class", "title": "An S4 class for continuous responses within an 'OmicsPathway' object", "topics": [ "OmicsReg-class" ] }, { "page": "OmicsSurv-class", "title": "An S4 class for survival responses within an 'OmicsPathway' object", "topics": [ "OmicsSurv-class" ] }, { "page": "pathwayPCA-package", "title": "Extract and Test the Significance of Pathway-Specific Principal Components", "topics": [ "pathwayPCA" ] }, { "page": "read_gmt", "title": "Read a '.gmt' file in as a 'pathwayCollection' object", "topics": [ "read_gmt" ] }, { "page": "SE2Tidy", "title": "Tidy a SummarizedExperiment Assay", "topics": [ "SE2Tidy" ] }, { "page": "get_set_OmicsPathway", "title": "Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects", "topics": [ "getAssay", "getAssay,OmicsPathway-method", "getAssay<-", "getAssay<-,OmicsPathway-method", "getPathwayCollection", "getPathwayCollection,OmicsPathway-method", "getPathwayCollection<-", "getPathwayCollection<-,OmicsPathway-method", "getSampleIDs", "getSampleIDs,OmicsPathway-method", "getSampleIDs<-", "getSampleIDs<-,OmicsPathway-method", "getTrimPathwayCollection", "getTrimPathwayCollection,OmicsPathway-method", "SubsetOmicsPath" ] }, { "page": "get_set_OmicsRegCateg", "title": "Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object", "topics": [ "getResponse", "getResponse,OmicsPathway-method", "getResponse<-", "getResponse<-,OmicsPathway-method", "SubsetOmicsResponse" ] }, { "page": "get_set_OmicsSurv", "title": "Access and Edit Event Time or Indicator in an 'OmicsSurv' Object", "topics": [ "getEvent", "getEvent,OmicsSurv-method", "getEvent<-", "getEvent<-,OmicsSurv-method", "getEventTime", "getEventTime,OmicsSurv-method", "getEventTime<-", "getEventTime<-,OmicsSurv-method", "SubsetOmicsSurv" ] }, { "page": "SubsetPathwayCollection", "title": "Subset a 'pathwayCollection'-class Object by Pathway.", "topics": [ "SubsetPathwayCollection", "[[.pathwayCollection" ] }, { "page": "SubsetPathwayData", "title": "Subset Pathway-Specific Data", "topics": [ "SubsetPathwayData", "SubsetPathwayData,OmicsPathway-method" ] }, { "page": "SuperPCA_pVals", "title": "Test pathways with Supervised PCA", "topics": [ "SuperPCA_pVals", "SuperPCA_pVals,OmicsPathway-method" ] }, { "page": "TransposeAssay", "title": "Transpose an Assay (Data Frame)", "topics": [ "TransposeAssay" ] }, { "page": "WhichPathways", "title": "Filter and Subset a 'pathwayCollection'-class Object by Symbol.", "topics": [ "WhichPathways" ] }, { "page": "wikipwsHS_Entrez_pathwayCollection", "title": "Wikipathways Homosapiens EntrezIDs", "topics": [ "wikipwsHS_Entrez_pathwayCollection" ] }, { "page": "wikipwsHS_Symbol_pathwayCollection", "title": "Wikipathways Homosapiens Gene Symbols", "topics": [ "wikipwsHS_Symbol_pathwayCollection" ] }, { "page": "write_gmt", "title": "Write a 'pathwayCollection' Object to a '.gmt' File", "topics": [ "write_gmt" ] } ], "_readme": "https://github.com/bioc/pathwayPCA/raw/HEAD/README.md", "_rundeps": [ "lars", "lattice", "Matrix", "survival" ], "_vignettes": [ { "source": "Introduction_to_pathwayPCA.Rmd", "filename": "Introduction_to_pathwayPCA.html", "title": "Integrative Pathway Analysis with pathwayPCA", "author": "Gabriel Odom, Lily Wang, Xi Chen", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "Installing the Package", "Stable Build", "Development Build", "Loading Packages", "2. Case study: identifying significant pathways in protein expressions associated with survival outcome in ovarian cancer data", "2.1. Ovarian cancer dataset", "2.2. Creating an Omics data object for pathway analysis", "2.2.1 Expression and Phenotype Data", "2.2.2 Pathway Collections", "2.2.3 Create an OmicsSurv Data Container", "2.3. Testing pathway association with phenotypes", "2.3.1 Method Description", "2.3.2 Implementation", "2.3.3 The pathway analysis results", "2.3.4 Extract relevant genes from significant pathways", "2.3.5 Subject-specific PCA estimates", "2.3.6 Extract analysis dataset for significant pathways", "3. Case study: an integrative multi-omics pathway analysis of ovarian cancer data", "3.1 Creating copy number Omics data object for pathway analysis", "3.2 Identifying significant pathways and relevant genes in both CNV and protein level", "3.3 An integrative view on patient-specific pathway activities", "4. Case study: analysis of studies with complex designs", "4.1 Data setup and AESPCA analysis", "4.2 Test for sex interaction with first PC", "4.3 Survival curves by sex interaction", "5. Further reading", "6. References" ], "created": "2018-12-14 00:43:20", "modified": "2020-11-30 19:08:12", "commits": 23 }, { "source": "Supplement1-Quickstart_Guide.Rmd", "filename": "Supplement1-Quickstart_Guide.html", "title": "Suppl. Ch. 1 - Quickstart Guide for New R Users", "author": "Gabriel Odom", "engine": "knitr::rmarkdown", "headings": [ "1. Overview", "Installing the Package", "Stable Build", "Development Build", "Loading Packages", "2. Import Data", "2.1 Import .gmt Files", "2.2 Import and Tidy Assay Data", "2.3 Import Phenotype Info", "2.4 Match the Phenotype and Assay Data", "3. Create an Omics Data Object", "3.1 Create an Object", "3.2 Inspect the Object", "3.3 Detailed Object Views", "3.3.1 View the Assay", "3.3.2 View the pathwayCollection List", "3.3.3 View the Event Time", "3.3.4 View the Event Indicator", "4. Test Pathways for Significance", "4.1 AES-PCA", "4.2 Supervised PCA", "5. Inspect Results", "5.1 Analysis Output Table", "5.2 Graph of Top Pathways", "5.2.1 Tidy Up the Data", "5.2.2 Graph Pathway Ranks", "6. Links to Detailed Information" ], "created": "2018-12-14 00:43:20", "modified": "2019-04-15 20:19:09", "commits": 3 }, { "source": "Supplement2-Importing_Data.Rmd", "filename": "Supplement2-Importing_Data.html", "title": "Suppl. Ch. 2 - Import and Tidy Data", "author": "Gabriel Odom", "engine": "knitr::rmarkdown", "headings": [ "1. Overview", "2. GMT Files", "2.1 GMT Format Description", "2.2 Import GMT files with read_gmt", "2.3 Creating Your Own pathwayCollection List", "2.4 Importing a Pathway Collection from Wikipathways", "2.4 Writing a pathwayCollection Object to a .gmt File", "3. Import and Tidy an Assay Matrix", "3.1 Import with readr", "3.2 Tidy the Assay Data Frame", "3.3 Subsetting a Tidy Data Frame", "3.4 Data from a SummarizedExperiment Object", "4. Import and Join Response Data", "5. Example Tidy Assay and Pathways List", "6. Review" ], "created": "2018-12-14 00:43:20", "modified": "2022-01-15 00:02:10", "commits": 8 }, { "source": "Supplement3-Create_Omics_Objects.Rmd", "filename": "Supplement3-Create_Omics_Objects.html", "title": "Suppl. Ch. 3 - Creating Data Objects", "author": "Gabriel Odom", "engine": "knitr::rmarkdown", "headings": [ "1. Overview", "1.1 Outline", "1.2 Import Data", "2. Omics-Class Objects Defined", "2.1 Class Overview", "2.2 Review of Data Types in R", "3. Create New Omics Objects", "3.1 Overview of Subtypes", "3.2 Create a Survival Omics Data Object", "3.3 View the New Object", "3.4 Regression and Classification Omics Data Objects", "4. Inspecting and Editing Omics-Class Objects", "4.1 Example \"Get\" Function", "4.2 Example \"Set\" Function", "4.3 Table of Accessors", "4.4 Inspect the Updated pathwayCollection List", "5. Review" ], "created": "2018-12-14 00:43:20", "modified": "2019-04-15 20:19:09", "commits": 2 }, { "source": "Supplement4-Methods_Walkthrough.Rmd", "filename": "Supplement4-Methods_Walkthrough.html", "title": "Suppl. Ch. 4 - Test Pathway Significance", "author": "Gabriel Odom", "engine": "knitr::rmarkdown", "headings": [ "1. Overview", "1.1 Outline", "1.2 Load Packages", "1.3 Load Omics Data", "2. Pathway Testing Setup", "2.1 Pathway Significance Testing Overview", "2.2 Extract Pathway PCs", "2.3 Test Pathway Association", "2.4 Adjust the Pathway $p$-Values for FDR", "2.5 Output a Sorted Data Frame / Tibble", "3. AES-PCA", "3.1 Method Details", "3.1.1 AES-PCA Method Sources", "3.1.2 Calculate Pathway-Specific Model $p$-Values", "3.1.3 AES-PCA Pros and Cons", "3.2 AES-PCA Examples", "3.2.1 Survival Response", "3.2.2 Regression Response", "3.2.3 Binary Classification Response", "4. Supervised PCA", "4.1 Method Details", "4.1.1 Supervised PCA Method Sources", "4.1.2 Calculate Pathway-Specific Model $p$-Values", "4.1.3 Supervised-PCA Pros and Cons", "4.2 Supervised PCA Examples", "4.2.1 Survival Response", "4.2.2 Regression Response", "4.2.3 Binary Classification Response", "5. Inspect the Results", "5.1 Table of $p$-Values", "5.2 Pathway PC and Loading Vectors", "6. Review" ], "created": "2018-12-14 00:43:20", "modified": "2019-04-15 20:19:09", "commits": 3 }, { "source": "Supplement5-Analyse_Results.Rmd", "filename": "Supplement5-Analyse_Results.html", "title": "Suppl. Ch. 5 - Visualizing the Results", "author": "Gabriel Odom", "engine": "knitr::rmarkdown", "headings": [ "1. Overview", "1.1 Packages", "1.2 Example Results", "2. Plot Pathway Significance Levels", "2.1 Trim Pathway Names", "2.2 Tidy the Pathway Results", "2.3 Plot Significant Survival Pathways for One Adjustment", "2.4 Plot Significant Survival Pathways for All Adjustments", "3. Inspecting the Driving Genes", "3.1 Extract Pathway Decomposition", "3.2 Gene Loadings", "3.2.1 Wrangle Pathway Loadings", "3.2.2 Plot the Gene Loadings", "3.3 Gene Correlations with PCs", "3.3.1 Calculate Pathway Correlations", "3.3.2 Plot the Assay-PC Correlation", "4. Plot patient-specific pathway activities", "5. 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