version 0.1.1

cran · Jul 14, 2023 · 8e16b34 · 8e16b34
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,39 +1,39 @@
 Package: RCPA
 Type: Package
 Title: Consensus Pathway Analysis
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
     person(given = "Zeynab", family = "Maghsoudi", email = "zmaghsoudi@nevada.unr.edu", role = c("aut", "cre")),
     person(given = "Phi Hung", family = "Bya", role = c("aut")),
     person(given = "Tin", family = "Nguyen", role = c("fnd")))
 Description: Consensus Pathway Analysis provides a set of functions to perform pathway analysis and meta analysis from multiple gene expression datasets, as well as visualization of the results.
     The package is wrapper of packages listed below.
-    Ritchie et al. (2015) <doi:10.1093/nar/gkv007>.
-    Love et al. (2014) <doi:10.1186/s13059-014-0550-8>.
-    Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>.
-    Korotkevich et al. (2016) <arxiv:10.1101/060012>.
-    Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>.
-    Gu, Z. (2012) <https://CRAN.R-project.org/package=CePa>.
+    'Ritchie et al'. (2015) <doi:10.1093/nar/gkv007>.
+    'Love et al'. (2014) <doi:10.1186/s13059-014-0550-8>.
+    'Robinson et al'. (2010) <doi:10.1093/bioinformatics/btp616>.
+    'Korotkevich et al'. (2016) <arxiv:10.1101/060012>.
+    'Efron et al'. (2015) <https://CRAN.R-project.org/package=GSA>.
+    'Gu, Z'. (2012) <https://CRAN.R-project.org/package=CePa>.
 License: GPL-3
 Encoding: UTF-8
-Depends: R (>= 4.0), methods, tidyr, dplyr, ggplot2, utils, stats
-biocViews: Biobase, DESeq2, GEOquery, affy, affyPLM, edgeR, limma,
-        RCyjs, fgsea, BrowserViz, oligo, SummarizedExperiment,
-        AnnotationDbi, ROntoTools
+Depends: R (>= 4.0), tidyr, dplyr, ggplot2, utils, stats
+biocViews: Biobase, DESeq2, GEOquery, edgeR, limma, RCyjs, fgsea,
+        BrowserViz, SummarizedExperiment, AnnotationDbi, ROntoTools
 Imports: AnnotationDbi, SummarizedExperiment, BiocManager, Biobase,
-        DESeq2, GEOquery, affy, affyPLM, edgeR, limma, oligo, stringr,
-        ggnewscale, ggrepel, graph, httr, rlang, ggpattern, scales
+        DESeq2, GEOquery, edgeR, limma, stringr, ggnewscale, ggrepel,
+        graph, httr, rlang, ggpattern, scales, RobustRankAggreg
 RoxygenNote: 7.2.3
-Suggests: knitr, testthat (>= 3.0.0), ROntoTools, RCyjs, fgsea,
-        BrowserViz, GSA, CePa, meta, png, ggvenn, RCurl, XML,
-        S4Vectors, devtools, hgu133plus2.db, org.Hs.eg.db
+Suggests: knitr, rmarkdown, markdown, testthat (>= 3.0.0), ROntoTools,
+        RCyjs, fgsea, BrowserViz, GSA, CePa, meta, png, ggvenn, RCurl,
+        XML, S4Vectors, devtools, hgu133plus2.db, org.Hs.eg.db, oligo
 Config/testthat/edition: 3
 Config/testthat/stop-on-test-error: false
+BugReports: https://github.com/tinnlab/RCPA/issues
 NeedsCompilation: no
-Packaged: 2023-05-11 01:27:21 UTC; zmaghsoudi
+Packaged: 2023-07-10 00:40:32 UTC; zmaghsoudi
 Author: Zeynab Maghsoudi [aut, cre],
   Phi Hung Bya [aut],
   Tin Nguyen [fnd]
 Maintainer: Zeynab Maghsoudi <zmaghsoudi@nevada.unr.edu>
 Repository: CRAN
-Date/Publication: 2023-05-11 10:10:08 UTC
+Date/Publication: 2023-07-13 21:30:11 UTC
diff --git a/MD5 b/MD5
@@ -1,67 +1,49 @@
-3ab808d487556ed2c4d202e7f9aac96f *DESCRIPTION
-0f3016dcdbf7de66795244b8ccee6748 *NAMESPACE
-92cf773ba0f0ebca160556cf723d8089 *R/CePa-helper.R
-60405fe09b624eedb4df50e3d65c4e12 *R/DE-analysis.R
-6ebfe23da86139992366fdbe0ff31a1a *R/GEO-download.R
-31053de58e51aa6e7a07c4ffb4bd2e44 *R/ID-mapping.R
-252f93d1db8f334c473900d791b6aa67 *R/SPIA-helper.R
-0a36887c378a0a48c75a06b090fad11e *R/annotation.R
-1a9ebfe559f3d5706d7f963a821434d8 *R/geneset-analysis.R
+637ecbe72d1fb5e1aeb3abaaf365159d *DESCRIPTION
+5827ab3436ea505e5550d30510c49f7b *NAMESPACE
+2af90237e4e6a094b6289f4a35f2d99e *R/CePa-helper.R
+0eb9bf95fbec51ec28a6a9d57fe7f138 *R/DE-analysis.R
+45111aae30139d0b33a0b9d25fa298ca *R/GEO-download.R
+44b99cc43d9d081ef46668dd7f089a05 *R/ID-mapping.R
+1107be81536271dbe46ecf3717897981 *R/SPIA-helper.R
+3775d34f64dcecd59fc5236bd9020194 *R/annotation.R
+64d5dce01cdbfaca4f2a30d8f3c8d096 *R/consensus-analysis.R
+b496a4677dec7af03f2b91f022488e82 *R/geneset-analysis.R
 cd312dafaf4d24ee286db8f0cd88e89a *R/genesets.R
-60f565e95474269c8595cc10e7d441a2 *R/global.R
-ccecc09a8ef046f1f748f90b5f24b2ca *R/meta-analysis.R
-ba089dc23618999241cfb407b9508d56 *R/pathway-analysis.R
-800b2bfacbf0db35b675b61c29037385 *R/plot-KEGG-map.R
-ddb367f7a13591bd0cd39c017a031e14 *R/plot-MA.R
+63ca3b5713bf10f855b3737e84135590 *R/global.R
+398c99503556b7701c3e7c939ef07e1d *R/meta-analysis.R
+dcdfbf14acae088c6839540aef65c472 *R/pathway-analysis.R
+81b6a0cb87db66491d3e1bae1fbe607c *R/plot-KEGG-map.R
+5c675fe80f0b749ec11c92e96931e40d *R/plot-MA.R
 e73365486f159a382f1bdfcdd5539582 *R/plot-forest.R
-9572ba80062b453a495b3a98eea2b502 *R/plot-gene-heatmap.R
+74008fc60aafce27ddaf3dd5ed451808 *R/plot-gene-heatmap.R
 b3b4d1a9defd8d6a831ee1e27fd024bb *R/plot-pathway-bar-chart.R
-f46577c733338a08eb699eb97d221e7a *R/plot-pathway-heatmap.R
-a280ab81e5bf8bb6a673ee5e5e7a43b4 *R/plot-pathway-network.R
-cbff01988eeb9425bb1bca76d6b11246 *R/plot-venn.R
+7b34df96cbfcbac1f4c5fe922c96fc31 *R/plot-pathway-heatmap.R
+8a2a908461fa0f7f857799cf0d8fedf5 *R/plot-pathway-network.R
+96176f2aa58c55b2cee36f285d2fd2e3 *R/plot-venn.R
 d7b06d561936dfc0ef42b08c3eecc34e *R/plot-volcano.R
-62acee878bee092577b7e31bcf32d2d7 *R/utils.R
+fd0a1bbfd3cd861baf9c6042bb833a19 *R/utils.R
 11640013126fc8c3ac82fc08e6a91694 *inst/extdata/pieStyle.js
-5f83bee30f913c6b8d932eb3c4205ac7 *man/combineDEAnalysisResults.Rd
-8bcbad6d15534473a60b7287429d6817 *man/combineEnrichmentAnalysisResults.Rd
-c139cc7324b8aefc70e99ef99f6ee969 *man/downloadGEO.Rd
+d9d8f3cc4d99d053044b353e8e53bb14 *man/downloadGEO.Rd
 8aa282c1acc5d380b81659acc0946b9b *man/getCePaPathwayCatalogue.Rd
 f2f448b3f673eb0c8b00bd7bfc741d31 *man/getEntrezAnnotation.Rd
 2ddda553dfc299ef821b8a1e90f9c1d4 *man/getGeneSets.Rd
 729ba2fcffc937d87564b7d6dc2dfe8c *man/getSPIAKEGGNetwork.Rd
 d943c4b5f812d712bb7617eb53115745 *man/getSupportedPlatforms.Rd
 591d81e03098a40e0aae459b8762b7a2 *man/loadData.Rd
 aa483bcfd5c00a91035e42b7412c7985 *man/plotBarChart.Rd
-14f605756337578cc53019eda82aed18 *man/plotDEGeneHeatmap.Rd
+700ef9eeca95ec7ffcf6480d5767758d *man/plotDEGeneHeatmap.Rd
 6ee6fdfbc73f90da3a56feae6e85d273 *man/plotForest.Rd
-0f14136dd64ab2d725c76af804463b52 *man/plotKEGGMap.Rd
+4be711c5ba063d2d1314a480aa941cdb *man/plotKEGGMap.Rd
 b2a8cecbd8cda2ad122e75e85f90ec77 *man/plotMA.Rd
 9279b19991284d212c2d41f0bcde4ec6 *man/plotPathwayHeatmap.Rd
-f96de11468440a2d535deb44cfbbba5c *man/plotPathwayNetwork.Rd
-e37d56fe6b69271681718343e957ec48 *man/plotVennDE.Rd
-0290d4e542d61cf44f18370f4c4b6096 *man/plotVennPathway.Rd
+7b168b9e065f2de754690905cd3ca9d8 *man/plotPathwayNetwork.Rd
+f2afb2ceee508fe9ebce0cad9e63e189 *man/plotVennDE.Rd
+a6ea6ca03747d922c36cebeb451071b0 *man/plotVennPathway.Rd
 8c20a94407359d83faa089a70d490a52 *man/plotVolcanoDE.Rd
 de357998a282cbd83648505dbb4f9eab *man/plotVolcanoPathway.Rd
-aa90304c5ee287d23902443e63f5e4c4 *man/runDEAnalysis.Rd
+a920603ab43617980c801cc6db78416a *man/runConsensusAnalysis.Rd
+65ed512b89ef7bb60bae376edcc6137b *man/runDEAnalysis.Rd
+81c6c091527585887be4e53b39daa984 *man/runDEMetaAnalysis.Rd
 89ecd38bdf3ef69f87e2eea991d5fd80 *man/runGeneSetAnalysis.Rd
-653db414717a9794e3d2896be3173580 *man/runPathwayAnalysis.Rd
-5862e9cb85e3938e810cf0cf6a8ee4d2 *tests/testthat.R
-aa0510d576353187dfe74041e1376c4c *tests/testthat/test-DE-analysis-helper.R
-07075f214c7a77c3f27bdd4c6213cb51 *tests/testthat/test-DE-analysis.R
-a51ac6a158ff8e9e963ac5b58c5eac55 *tests/testthat/test-GEO-download.R
-9188672db666eb006ea39b24480502e0 *tests/testthat/test-entrez-annotation.R
-e8f62d9b9d39cffbaa94a1434472fde4 *tests/testthat/test-geneset-analysis.R
-9beaf372f048b4b550de73ecbfd87780 *tests/testthat/test-genesets.R
-f786065b9f223e84dd9fb5af8f0e6aa5 *tests/testthat/test-id-mapping.R
-1d1961e6b9008893e4064677aaeaf174 *tests/testthat/test-meta-analysis.R
-f640249c58745070fdef293058f61b08 *tests/testthat/test-pathway-analysis.R
-6685717701febe2f809eef7b1a2670aa *tests/testthat/test-plot-DE-gene-heatmap.R
-1cb35c468045ab3c3569a2ce4b25d59f *tests/testthat/test-plot-KEGG-map.R
-d194455e9b5fa919fe1c29baabd1b31f *tests/testthat/test-plot-MA.R
-58bdb79efc5fa667fd21b93d9dcce301 *tests/testthat/test-plot-forest.R
-323185556cbec91ace84f1fce54dbd20 *tests/testthat/test-plot-pathway-bar-chart.R
-885deea4f4e8248536fd35545e0a8d25 *tests/testthat/test-plot-pathway-heatmap.R
-bcf9e05e8981171f1dd1592b55b72891 *tests/testthat/test-plot-pathway-network.R
-5e6d190fd5f80dd8a8ef9e2a66d28fb2 *tests/testthat/test-plot-venn-DE.R
-1faf97635ab01345a83c2bc6274a46ee *tests/testthat/test-plot-volcano-DE.R
-5aceeed55c451d14a347b9b1fce5774c *tests/testthat/test-plot-volcano-pathway.R
+c927928cdd389237ec889b42caec2e40 *man/runPathwayAnalysis.Rd
+300f0645a902c437254d30c5d22678a8 *man/runPathwayMetaAnalysis.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,7 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(combineDEAnalysisResults)
-export(combineEnrichmentAnalysisResults)
 export(downloadGEO)
 export(getCePaPathwayCatalogue)
 export(getEntrezAnnotation)
@@ -20,9 +18,12 @@ export(plotVennDE)
 export(plotVennPathway)
 export(plotVolcanoDE)
 export(plotVolcanoPathway)
+export(runConsensusAnalysis)
 export(runDEAnalysis)
+export(runDEMetaAnalysis)
 export(runGeneSetAnalysis)
 export(runPathwayAnalysis)
+export(runPathwayMetaAnalysis)
 importFrom(AnnotationDbi,keys)
 importFrom(Biobase,annotation)
 importFrom(Biobase,exprs)
@@ -33,12 +34,12 @@ importFrom(DESeq2,DESeqDataSetFromMatrix)
 importFrom(DESeq2,results)
 importFrom(GEOquery,getGEO)
 importFrom(GEOquery,getGEOSuppFiles)
+importFrom(RobustRankAggreg,aggregateRanks)
+importFrom(RobustRankAggreg,rankMatrix)
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
-importFrom(affy,ReadAffy)
-importFrom(affyPLM,threestep)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
@@ -118,6 +119,7 @@ importFrom(graph,addEdge)
 importFrom(graph,edges)
 importFrom(graph,graphNEL)
 importFrom(graph,nodes)
+importFrom(httr,HEAD)
 importFrom(httr,POST)
 importFrom(httr,content)
 importFrom(limma,backgroundCorrect)
@@ -129,10 +131,8 @@ importFrom(limma,normalizeBetweenArrays)
 importFrom(limma,normalizeWithinArrays)
 importFrom(limma,read.maimages)
 importFrom(limma,topTable)
-importFrom(methods,setGeneric)
-importFrom(oligo,read.celfiles)
-importFrom(oligo,rma)
 importFrom(rlang,.data)
+importFrom(rlang,is_interactive)
 importFrom(rlang,sym)
 importFrom(scales,trans_new)
 importFrom(stats,ks.test)
@@ -145,6 +145,7 @@ importFrom(stats,phyper)
 importFrom(stats,pnorm)
 importFrom(stats,qnorm)
 importFrom(stats,setNames)
+importFrom(stats,weighted.mean)
 importFrom(stats,wilcox.test)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_length)

diff --git a/R/CePa-helper.R b/R/CePa-helper.R
@@ -14,8 +14,12 @@
 #' @importFrom stringr str_split
 getCePaPathwayCatalogue <- function(org = "hsa", updateCache = FALSE){
 
-  .requirePackage("CePa")
-  .requirePackage("ROntoTools")
+  if (!.requirePackage("CePa")){
+    return(NULL)
+  }
+  if (!.requirePackage("ROntoTools")){
+    return(NULL)
+  }
 
   keggPathway <- ROntoTools::keggPathwayGraphs(org, updateCache = updateCache)
 

diff --git a/R/DE-analysis.R b/R/DE-analysis.R
@@ -111,15 +111,23 @@
 #' library(RCPA)
 #' library(SummarizedExperiment)
 #'
+#' #if (!require("hgu133plus2.db", quietly = TRUE)) {
+#'  #BiocManager::install("hgu133plus2.db")
+#' #}
+#' #library(hgu133plus2.db)
+#'
 #' # GSE5281
 #' affyDataset <- loadData("affyDataset")
 #' affyDesign <- model.matrix(~0 + condition + region + condition:region, data = colData(affyDataset))
 #' colnames(affyDesign) <- make.names(colnames(affyDesign))
 #' affyContrast <- limma::makeContrasts(conditionalzheimer-conditionnormal, levels=affyDesign)
 #'
+#' if (require("hgu133plus2.db", quietly = TRUE)){
 #' affyDEExperiment <- RCPA::runDEAnalysis(affyDataset, method = "limma", design = affyDesign,
 #'                                         contrast = affyContrast, annotation = "GPL570")
-#' print(rowData(affyDEExperiment)) # check the DE analysis results
+#' }
+#' # print(rowData(affyDEExperiment)) # check the DE analysis results
+#'
 #'
 #' # GSE61196
 #' agilDataset <- loadData("agilDataset")
@@ -134,27 +142,31 @@
 #'
 #' agilDEExperiment <- RCPA::runDEAnalysis(agilDataset, method = "limma", design = agilDesign,
 #'                                         contrast = agilContrast, annotation = GPL4133GeneMapping)
-#' print(rowData(agilDEExperiment))
+#' # print(rowData(agilDEExperiment))
 #'
 #' # GSE153873
 #' RNASeqDataset <- loadData("RNASeqDataset")
 #' RNASeqDesign <- model.matrix(~0 + condition, data = colData(RNASeqDataset))
 #' RNASeqContrast <- limma::makeContrasts(conditionalzheimer-conditionnormal, levels=RNASeqDesign)
 #'
 #' # Create mapping
-#' if (!require("org.Hs.eg.db", quietly = TRUE)) {
-#'     BiocManager::install("org.Hs.eg.db")
-#' }
+#' # Install org.Hs.eg.db if not installed
+#' # if (!require("org.Hs.eg.db", quietly = TRUE)) {
+#' #     BiocManager::install("org.Hs.eg.db")
+#' # }
 #'
-#' library(org.Hs.eg.db)
-#' ENSEMBLMapping <- AnnotationDbi::select(org.Hs.eg.db, keys = rownames(RNASeqDataset),
-#'                                         columns = c("SYMBOL", "ENTREZID"), keytype = "SYMBOL")
-#' colnames(ENSEMBLMapping) <- c("FROM", "TO")
-#'
-#' RNASeqDEExperiment <- RCPA::runDEAnalysis(RNASeqDataset, method = "DESeq2", design = RNASeqDesign,
-#'                                           contrast = RNASeqContrast, annotation = ENSEMBLMapping)
-#' print(rowData(RNASeqDEExperiment))
+#' if (require("org.Hs.eg.db", quietly = TRUE)){
+#'     ENSEMBLMapping <- AnnotationDbi::select(org.Hs.eg.db, keys = rownames(RNASeqDataset),
+#'                                             columns = c("SYMBOL", "ENTREZID"), keytype = "SYMBOL")
+#'     colnames(ENSEMBLMapping) <- c("FROM", "TO")
 #'
+#'     RNASeqDEExperiment <- RCPA::runDEAnalysis(RNASeqDataset,
+#'                            method = "DESeq2",
+#'                            design = RNASeqDesign,
+#'                            contrast = RNASeqContrast,
+#'                            annotation = ENSEMBLMapping)
+#'     # print(rowData(RNASeqDEExperiment))
+#' }
 #' }
 #' @importFrom SummarizedExperiment SummarizedExperiment rowData assay colData
 #' @importFrom dplyr %>%
@@ -171,7 +183,9 @@ runDEAnalysis <- function(summarizedExperiment, method = c("limma", "DESeq2", "e
         stop("Contrast matrix must be provided")
     }
 
-    .requirePackage("S4Vectors")
+    if (!.requirePackage("S4Vectors")){
+        return(NULL)
+    }
 
     # get ID mapping annotation
     if (is.null(annotation)) {
@@ -193,7 +207,9 @@ runDEAnalysis <- function(summarizedExperiment, method = c("limma", "DESeq2", "e
         stop("Annotation must be a data frame or a string")
     }
 
-    .requirePackage("S4Vectors")
+    if (is.null(annotation) & pkgEnv$isMissingDependency){
+        return(NULL)
+    }
 
     # get expression matrix
     exprs <- assay(summarizedExperiment)