getGenesets: update msigdb collections

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: EnrichmentBrowser
-Version: 2.21.8
+Version: 2.21.9
 Date: 2020-08-10
 Title: Seamless navigation through combined results of set-based and
        network-based enrichment analysis

R/getGenesets.R

@@ -1,4 +1,4 @@
-###############################################################################
+##############################################################################
 # 
 # Author: ludwig geistlinger
 # Date: 16 June 2010
@@ -68,7 +68,7 @@
 #' MSigDB collection category: 'H' (hallmark), 
 #' 'C1' (genomic position), 'C2' (curated databases), 'C3' (binding site motifs),
 #' 'C4' (computational cancer), 'C5' (Gene Ontology), 'C6' (oncogenic), 
-#' 'C7' (immunologic). See references. 
+#' 'C7' (immunologic), 'C8' (cell type). See references. 
 #' \item subcat: Character. MSigDB collection subcategory. Depends on the
 #' chosen MSigDB collection category. For example, 'MIR' to obtain microRNA targets
 #' from the 'C3' collection. See references.}
@@ -352,11 +352,15 @@ writeGMT <- function(gs, gmt.file)
 # MSigDB
 #
 .getMSigDb <- function(org, gene.id.type, cache, return.type,
-                        cat = c("H", paste0("C", 1:7)), 
+                        cat = c("H", paste0("C", 1:8)), 
                         subcat = NA)
 {
-    cat <- match.arg(cat)
-
+    isAvailable("msigdbr", type = "software")
+    supp.cats <- unique(msigdbr::msigdbr_collections()$gs_cat)
+    if(!(cat %in% supp.cats))
+        stop(gettextf("'cat' should be one of %s", 
+                      paste(dQuote(supp.cats), collapse = ", ")), domain = NA)
+
     gs.tag <- "gs"
     if(return.type == "GeneSetCollection") gs.tag <- paste0(gs.tag, "c")
 
@@ -372,7 +376,6 @@ writeGMT <- function(gs, gmt.file)
     ind <- match(org, SPECIES[,"kegg"])
     morg <- SPECIES[ind, "tax"]
 
-    isAvailable("msigdbr", type = "software")
     if(!(morg %in% msigdbr::msigdbr_species()$species_name)) 
         stop("Organism not supported")
 

R/getMicrobeSets.R

@@ -63,7 +63,7 @@ names(MPA.TAX.LEVELS) <- TAX.LEVELS
 
     # obtain study, experiment, and signature tables 
     einfo <- .getExpInfo()   
-    sigs <- read.csv("https://bugsigdb.org/Special:Ask/-5B-5BCategory:Signatures-5D-5D/-3FOriginal-20page-20name%3DSignature-20page-20name/-3FRelated-20experiment%3DExperiment/-3FRelated-20study%3DStudy/-3FSource-20data%3DSource/-3FCurated-20date/-3FCurator/-3FRevision-20editor/-3FDescription/-3FAbundance-20in-20Group-201/-3FNCBI-20export%3DMetaPhlAn-20taxon-20names/-3FNCBI-20export-20ids%3DNCBI-20Taxonomy-20IDs/mainlabel%3D-2D/limit%3D5000/offset%3D0/format%3Dcsv/searchlabel%3DDownload-20all-20Signatures-20(CSV)/filename%3Dsignatures.csv")
+    sigs <- read.csv("https://tinyurl.com/yakgsowm")
 
     # extract signatures
     snames <- .makeSigNames(sigs, einfo) 
@@ -178,7 +178,7 @@ names(MPA.TAX.LEVELS) <- TAX.LEVELS
 
 .getExpInfo <- function()
 {
-    exps <- read.csv("https://bugsigdb.org/w/index.php?title=Special:Ask&x=-5B-5BCategory%3AExperiments-5D-5D%2F-3FOriginal-20page-20name%3DExperiment-20page-20name%2F-3FRelated-20study%3DStudy%2F-3FLocation-20of-20subjects%2F-3FHost-20species%2F-3FBody-20site%2F-3FCondition%2F-3FGroup-200-20name%2F-3FGroup-201-20name%2F-3FGroup-201-20definition%2F-3FGroup-200-20sample-20size%2F-3FGroup-201-20sample-20size%2F-3FAntibiotics-20exclusion%2F-3FSequencing-20type%2F-3F16s-20variable-20region%2F-3FSequencing-20platform%2F-3FStatistical-20test%2F-3FSignificance-20threshold%2F-3FMHT-20correction%2F-3FLDA-20Score-20above%2F-3FMatched-20on%2F-3FConfounders-20controlled-20for%2F-3FPielou%2F-3FShannon%2F-3FChao1%2F-3FSimpson%2F-3FInverse-20Simpson%2F-3FRichness&mainlabel=-&limit=5000&order=asc&sort=Page%20sort%20number&offset=0&format=csv&searchlabel=Download%20all%20Experiments%20%28CSV%29&filename=experiments.csv")
+    exps <- read.csv("https://tinyurl.com/yb2fmpa3")
 
     is.study <- grepl("^Study [0-9]+$", exps[["Study"]])
     is.exp <- grepl("^Experiment [0-9]+$", exps[["Experiment.page.name"]])
@@ -201,7 +201,7 @@ names(MPA.TAX.LEVELS) <- TAX.LEVELS
 
 .study2pmid <- function()
 {
-    studs <- read.csv("https://bugsigdb.org/Special:Ask/-5B-5BCategory:Studies-5D-5D/-3FStudy-20design/-3FPMID/-3FDOI/-3FURL/-3FAuthors/-3FTitle/-3FJournal/-3FYear/-3FAbstract/mainlabel%3DStudy-20page-20name/limit%3D5000/order%3Dasc/sort%3DPage-20sort-20number/offset%3D0/format%3Dcsv/searchlabel%3DDownload-20all-20Studies-20(CSV)/filename%3Dstudies.csv")
+    studs <- read.csv("https://tinyurl.com/ycg8fs9x")
 
     s2pmid <- studs[["PMID"]]
     names(s2pmid) <- studs[["Study.page.name"]]