version 0.1.0

DESCRIPTION

@@ -0,0 +1,39 @@
+Package: RCPA
+Type: Package
+Title: Consensus Pathway Analysis
+Version: 0.1.0
+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>.
+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
+Imports: AnnotationDbi, SummarizedExperiment, BiocManager, Biobase,
+        DESeq2, GEOquery, affy, affyPLM, edgeR, limma, oligo, stringr,
+        ggnewscale, ggrepel, graph, httr, rlang, ggpattern, scales
+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
+Config/testthat/edition: 3
+Config/testthat/stop-on-test-error: false
+NeedsCompilation: no
+Packaged: 2023-05-11 01:27:21 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

MD5

@@ -0,0 +1,67 @@
+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
+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
+e73365486f159a382f1bdfcdd5539582 *R/plot-forest.R
+9572ba80062b453a495b3a98eea2b502 *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
+d7b06d561936dfc0ef42b08c3eecc34e *R/plot-volcano.R
+62acee878bee092577b7e31bcf32d2d7 *R/utils.R
+11640013126fc8c3ac82fc08e6a91694 *inst/extdata/pieStyle.js
+5f83bee30f913c6b8d932eb3c4205ac7 *man/combineDEAnalysisResults.Rd
+8bcbad6d15534473a60b7287429d6817 *man/combineEnrichmentAnalysisResults.Rd
+c139cc7324b8aefc70e99ef99f6ee969 *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
+6ee6fdfbc73f90da3a56feae6e85d273 *man/plotForest.Rd
+0f14136dd64ab2d725c76af804463b52 *man/plotKEGGMap.Rd
+b2a8cecbd8cda2ad122e75e85f90ec77 *man/plotMA.Rd
+9279b19991284d212c2d41f0bcde4ec6 *man/plotPathwayHeatmap.Rd
+f96de11468440a2d535deb44cfbbba5c *man/plotPathwayNetwork.Rd
+e37d56fe6b69271681718343e957ec48 *man/plotVennDE.Rd
+0290d4e542d61cf44f18370f4c4b6096 *man/plotVennPathway.Rd
+8c20a94407359d83faa089a70d490a52 *man/plotVolcanoDE.Rd
+de357998a282cbd83648505dbb4f9eab *man/plotVolcanoPathway.Rd
+aa90304c5ee287d23902443e63f5e4c4 *man/runDEAnalysis.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

NAMESPACE

@@ -0,0 +1,162 @@
+# Generated by roxygen2: do not edit by hand
+
+export(combineDEAnalysisResults)
+export(combineEnrichmentAnalysisResults)
+export(downloadGEO)
+export(getCePaPathwayCatalogue)
+export(getEntrezAnnotation)
+export(getGeneSets)
+export(getSPIAKEGGNetwork)
+export(getSupportedPlatforms)
+export(loadData)
+export(plotBarChart)
+export(plotDEGeneHeatmap)
+export(plotForest)
+export(plotKEGGMap)
+export(plotMA)
+export(plotPathwayHeatmap)
+export(plotPathwayNetwork)
+export(plotVennDE)
+export(plotVennPathway)
+export(plotVolcanoDE)
+export(plotVolcanoPathway)
+export(runDEAnalysis)
+export(runGeneSetAnalysis)
+export(runPathwayAnalysis)
+importFrom(AnnotationDbi,keys)
+importFrom(Biobase,annotation)
+importFrom(Biobase,exprs)
+importFrom(Biobase,pData)
+importFrom(BiocManager,install)
+importFrom(DESeq2,DESeq)
+importFrom(DESeq2,DESeqDataSetFromMatrix)
+importFrom(DESeq2,results)
+importFrom(GEOquery,getGEO)
+importFrom(GEOquery,getGEOSuppFiles)
+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)
+importFrom(dplyr,desc)
+importFrom(dplyr,filter)
+importFrom(dplyr,first)
+importFrom(dplyr,group_by)
+importFrom(dplyr,group_split)
+importFrom(dplyr,inner_join)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
+importFrom(dplyr,summarize_all)
+importFrom(edgeR,DGEList)
+importFrom(edgeR,calcNormFactors)
+importFrom(edgeR,estimateDisp)
+importFrom(edgeR,glmQLFTest)
+importFrom(edgeR,glmQLFit)
+importFrom(edgeR,topTags)
+importFrom(ggnewscale,new_scale_fill)
+importFrom(ggpattern,geom_bar_pattern)
+importFrom(ggpattern,scale_pattern_manual)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,annotation_custom)
+importFrom(ggplot2,annotation_raster)
+importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,coord_flip)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,expansion)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_errorbarh)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_rect)
+importFrom(ggplot2,geom_smooth)
+importFrom(ggplot2,geom_text)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_vline)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,guide_colorbar)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,margin)
+importFrom(ggplot2,scale_color_gradient)
+importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,scale_colour_discrete)
+importFrom(ggplot2,scale_fill_continuous)
+importFrom(ggplot2,scale_fill_discrete)
+importFrom(ggplot2,scale_fill_gradient)
+importFrom(ggplot2,scale_fill_gradient2)
+importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_size)
+importFrom(ggplot2,scale_size_continuous)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_discrete)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,scale_y_discrete)
+importFrom(ggplot2,sec_axis)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_minimal)
+importFrom(ggplot2,theme_void)
+importFrom(ggplot2,unit)
+importFrom(ggrepel,geom_label_repel)
+importFrom(grDevices,colorRampPalette)
+importFrom(graph,`nodeData<-`)
+importFrom(graph,`nodeDataDefaults<-`)
+importFrom(graph,addEdge)
+importFrom(graph,edges)
+importFrom(graph,graphNEL)
+importFrom(graph,nodes)
+importFrom(httr,POST)
+importFrom(httr,content)
+importFrom(limma,backgroundCorrect)
+importFrom(limma,contrasts.fit)
+importFrom(limma,eBayes)
+importFrom(limma,lmFit)
+importFrom(limma,makeContrasts)
+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,sym)
+importFrom(scales,trans_new)
+importFrom(stats,ks.test)
+importFrom(stats,median)
+importFrom(stats,model.matrix)
+importFrom(stats,na.omit)
+importFrom(stats,p.adjust)
+importFrom(stats,pchisq)
+importFrom(stats,phyper)
+importFrom(stats,pnorm)
+importFrom(stats,qnorm)
+importFrom(stats,setNames)
+importFrom(stats,wilcox.test)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_length)
+importFrom(stringr,str_match)
+importFrom(stringr,str_remove)
+importFrom(stringr,str_split)
+importFrom(stringr,str_split_1)
+importFrom(stringr,str_starts)
+importFrom(tidyr,drop_na)
+importFrom(tidyr,gather)
+importFrom(tidyr,spread)
+importFrom(utils,URLdecode)
+importFrom(utils,globalVariables)
+importFrom(utils,head)
+importFrom(utils,read.table)

R/CePa-helper.R

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+#' @title Get KEGG pathway catalouge (network) for CePa.ORA and CePa.GSA methods
+#' @description Get KEGG pathway catalouge for CePa.ORA and CePa.GSA methods
+#' @param org The organism abbreviation. E.g, hsa, mmu, dme, etc.
+#' To see the full list of supported organisms, visit https://www.genome.jp/kegg/catalog/org_list.html.
+#' @param updateCache A parameter to enable/disable cache update.
+#' @return A named list with three elements: network, names and sizes for CePa.ORA and CePa.GSA methods.
+#' @examples
+#' \donttest{
+#' getCePaPathwayCatalogue("hsa")
+#' }
+#' @export
+#' @importFrom graph nodes edges
+#' @importFrom dplyr %>% filter select group_by group_split
+#' @importFrom stringr str_split
+getCePaPathwayCatalogue <- function(org = "hsa", updateCache = FALSE){
+
+  .requirePackage("CePa")
+  .requirePackage("ROntoTools")
+
+  keggPathway <- ROntoTools::keggPathwayGraphs(org, updateCache = updateCache)
+
+  interactionList <- lapply(keggPathway, function(pathway){
+    pathway@edgeData %>% names()
+  }) %>% do.call(what=c) %>% unique()
+
+  pathList <- lapply(keggPathway, function(pathway){
+    (interactionList %in% (pathway@edgeData %>% names())) %>% which() %>% as.character()
+  })
+
+  interactionList <- seq(length(interactionList)) %>% as.character() %>% cbind(
+    interactionList %>% strsplit('\\|') %>% do.call(what=rbind)
+  ) %>% data.frame(stringsAsFactors = FALSE)
+
+  colnames(interactionList) <- c("interaction.id", "input", "output")
+  rownames(interactionList) <- interactionList$interaction.id
+
+  interactionList_modified <- interactionList
+  interactionList_modified$input <- interactionList$input %>% strsplit(":") %>% sapply(function(x) x[2]) %>% as.character()
+  interactionList_modified$output <- interactionList$output %>% strsplit(":") %>% sapply(function(x) x[2]) %>% as.character()
+
+  mapping <- lapply(keggPathway, function(pathway) pathway@nodes) %>% unlist() %>% unique()
+  mapping_modified <- mapping %>% strsplit(":") %>% sapply(function(x) x[2]) %>% as.character()
+  mapping_modified <- data.frame(node.id = mapping_modified, symbol = mapping_modified, stringsAsFactors = FALSE)
+
+  cat <- CePa::set.pathway.catalogue(pathList, interactionList_modified, mapping_modified, min.node = 2, max.node = 1e+6)
+
+  pathways_size <- cat[["pathList"]] %>% lapply(function (path) length(path)) %>% unlist() %>% as.vector()
+  names(pathways_size) <- names(cat[["pathList"]])
+
+  list(
+      network = cat,
+      names = .getKEGGPathwayNames(org)[names(cat$pathList)],
+      sizes = pathways_size
+  )
+}