Merge pull request YuLab-SMU#56 from huerqiang/updateData

Update data
allenlile · Nov 17, 2021 · bfcd25b · bfcd25b
2 parents cf47559 + 378be0e
commit bfcd25b
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Showing 15 changed files with 18 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.21.0
+Version: 3.21.0.991
 Authors@R: c( person(given = "Guangchuang", family = "Yu",        email = "[email protected]",   role = c("aut", "cre")),
               person(given = "Li-Gen",      family = "Wang",      email = "[email protected]",   role = "ctb"),
               person(given = "Vladislav",   family = "Petyuk",    email = "[email protected]",          role = "ctb"),
@@ -45,4 +45,4 @@ BugReports: https://github.com/GuangchuangYu/DOSE/issues
 Packaged: 2011-12-28 08:16:14 UTC; root
 biocViews: Annotation, Visualization, MultipleComparison, GeneSetEnrichment,
     Pathways, Software
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# DOSE 3.21.0.991
++ upate DisGeNET and NCG data (2021-11-14, Sun)
+
 # DOSE 3.19.4
 
 + update `clusterProfiler` citation (2021-09-30, Thu)

diff --git a/data/DGN_EXTID2PATHID.rda b/data/DGN_EXTID2PATHID.rda
diff --git a/data/DGN_PATHID2EXTID.rda b/data/DGN_PATHID2EXTID.rda
diff --git a/data/DGN_PATHID2NAME.rda b/data/DGN_PATHID2NAME.rda
diff --git a/data/DOIC.rda b/data/DOIC.rda
diff --git a/data/NCG_EXTID2PATHID.rda b/data/NCG_EXTID2PATHID.rda
diff --git a/data/NCG_PATHID2EXTID.rda b/data/NCG_PATHID2EXTID.rda
diff --git a/data/NCG_PATHID2NAME.rda b/data/NCG_PATHID2NAME.rda
diff --git a/data/VDGN_EXTID2PATHID.rda b/data/VDGN_EXTID2PATHID.rda
diff --git a/data/VDGN_PATHID2EXTID.rda b/data/VDGN_PATHID2EXTID.rda
diff --git a/data/VDGN_PATHID2NAME.rda b/data/VDGN_PATHID2NAME.rda
diff --git a/inst/extdata/buildAnnoData.R b/inst/extdata/buildAnnoData.R
@@ -1,8 +1,13 @@
+## do_rif.human.txt was downloaded from
+## http://projects.bioinformatics.northwestern.edu/do_rif/
+##
 do.rif <- read.delim2(gzfile("do_rif.human.txt.gz"), sep="\t",
                       stringsAsFactors=F, header=F)
 eg.do1 <- do.rif[,c(1,5)]
 colnames(eg.do1) <- c("eg", "doid")
 
+## IDMappings.txt from
+## http://doa.nubic.northwestern.edu/pages/download.php
 domapping <- read.delim(gzfile("IDMappings.txt.gz"), stringsAsFactors=F)
 eg.do2 <- domapping[,c(2,1)]
 colnames(eg.do2) <- c("eg", "doid")
@@ -13,3 +18,7 @@ eg.do <- unique(eg.do)
 
 
 DOSE:::rebuildAnnoData.internal(eg.do)
+
+# DOIC.rda 
+# for new slot `geneAnno` of object `GOSemSimDATA`
+DOSE:::build_dodata()
diff --git a/inst/extdata/build_NCG_Anno.R b/inst/extdata/build_NCG_Anno.R
@@ -1,5 +1,6 @@
 # download from http://ncg.kcl.ac.uk/download.php
-# All cancer genes -> •List of 2372 cancer genes and supporting literature
+# NCG 6.0: All cancer genes -> •List of 2372 cancer genes and supporting literature
+# NCG 7.0: List of all 3347 cancer drivers and their annotation and supporting evidence
 #x=read.delim("NCG6_cancergenes.tsv", stringsAsFactor=F)
 x=read.delim("NCG6_cancergenes.tsv", stringsAsFactor=F, encoding = "latin1")
 path2gene <- x[, c("cancer_type", "entrez")]

diff --git a/man/show-methods.Rd b/man/show-methods.Rd