@@ -1,12 +1,12 @@

 Package: rTRM

 Type: Package

 Title: Identification of transcriptional regulatory modules from PPI networks

-Version: 1.1.8

+Version: 1.1.9

 Date: 2014-02-14

 Author: Diego Diez

-Depends: R (>= 2.10), igraph, RSQLite, annotate

-Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8, org.Mm.eg.db

+Depends: R (>= 2.10), igraph, RSQLite

 Imports: AnnotationDbi

+Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8, org.Mm.eg.db

 Maintainer: Diego Diez <[email protected]>

 Description: rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

 License: GPL-3

@@ -1 +1,4 @@

+import(igraph,RSQLite)

+importMethodsFrom(AnnotationDbi,select)

+

 exportPattern("^[[:alpha:]]+")

@@ -105,8 +105,9 @@ getMotifsFromEntrezgene = function(e, organism) {

 # get corresponding motifs from entrezgene symbol

 getMotifsFromSymbol = function(s, organism) {

-  map = .getMapFromOrg(organism, "ALIAS2EG")

-  e = unlist(AnnotationDbi::mget(s, map))

+  map=.getMapFromOrg(organism)

+  res=select(map,keys=s,columns="ENTREZID",keytype="ALIAS")

+  e=unique(na.omit(res$ENTREZID))

   o = getOrthologs(organism = organism)

   e_map = unique(o$entrezgene[o$map_entrezgene == e])

@@ -15,10 +15,10 @@ initBiomart = function(filter, biomart = "ensembl", host) {

 }

-.getMapFromOrg = function(org, map = "SYMBOL") {

+.getMapFromOrg = function(org) {#, map = "SYMBOL") {

 	switch(org,

-		human = annotate::getAnnMap(map, "org.Hs.eg.db"),

-		mouse = annotate::getAnnMap(map, "org.Mm.eg.db")

+    human = get("org.Hs.eg.db"),

+    mouse = get("org.Mm.eg.db")

 	)

 }

@@ -35,8 +35,8 @@ getOrthologsFromBiomart = function(eg, target_org, mart) {

 	res = res[!is.na(res)]

 	res = unique(res[res != ""])

 	if(length(res) > 0) {

-		map = .getMapFromOrg(target_org, "ENSEMBL2EG")

-		res = unlist(AnnotationDbi::mget(res, map, ifnotfound = NA), use.names = FALSE)

-		unique(res[!is.na(res)])

+    map=.getMapFromOrg(target_org)

+    res=select(map,keys=res,columns="ENTREZID",keytype="ENSEMBL")

+		unique(na.omit(res$ENTREZID))

 	}

 }

@@ -30,26 +30,6 @@ getBiogridData = function(release) {

   list(db = db, release = release, date = Sys.Date())

 }

-# getBiogridData = function(release) {

-# 	tmp = tempfile()

-# 	file = paste("BIOGRID-ALL-", release, ".tab2", sep = "")

-# 	url = paste("http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-", release, "/", file, ".zip", sep = "")

-# 	download.file(url, destfile = tmp)

-# 	db = read.delim(unz(tmp, paste(file, ".txt", sep = "")), check.names = FALSE, colClasses = "character")

-# 	unlink(tmp)

-# 	list(db = db, release = release, date = Sys.Date())

-#}

-

-# getBiogridData = function(release) {

-# 	tmp = tempfile()

-# 	file = paste("BIOGRID-ALL-", release, ".tab2", sep = "")

-# 	url = paste("http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-", release, "/", file, ".zip", sep = "")

-# 	download.file(url, destfile = tmp)

-# 	db = read.delim(unz(tmp, paste(file, ".txt", sep = "")), check.names = FALSE, colClasses = "character")

-# 	unlink(tmp)

-# 	list(db = db, release = release, date = Sys.Date())

-#}

-

 processBiogrid = function(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE) {

   db = dblist$db

@@ -72,10 +52,11 @@ processBiogrid = function(dblist, org = "human", simplify = TRUE, type = "physic

   biogrid = graph.edgelist(dbtmp, directed = FALSE)

-  # add gene annotations

+  # add gene annotations  

   map = .getMapFromOrg(org)

-  sym = unlist(AnnotationDbi::mget(V(biogrid)$name, map, ifnotfound = NA))

-  sym[is.na(sym)] = paste("eg:", names(sym[is.na(sym)]), sep = "")

+  res = select(map, keys=V(biogrid)$name, columns="SYMBOL")

+  sym = res$SYMBOL

+  sym[is.na(sym)] = paste("eg:", res$ENTREZID[is.na(sym)], sep="")

   V(biogrid)$label = sym[V(biogrid)$name]

@@ -86,8 +67,6 @@ processBiogrid = function(dblist, org = "human", simplify = TRUE, type = "physic

   # create simplified graph.

   if (simplify) {

-    #E(biogrid)$biogrid_count <- count.multiple(biogrid)

-    #biogrid = simplify(biogrid)

     biogrid = igraph::simplify(biogrid,edge.attr.comb="concat")

     E(biogrid)$biogrid_count=sapply(E(biogrid)$pubmed_id,function(x) length(x))

   }

@@ -2,13 +2,14 @@

 writeTRMreport = function(graph, file, organism, target, query, sort.by = "symbol") {

 	x = V(graph)$name

-	smap = .getMapFromOrg(organism, "SYMBOL")

-	S = unlist(AnnotationDbi::mget(x, smap, ifnotfound = NA))

+  map=.getMapFromOrg(organism)

+  res=select(map,keys=x,columns=c("SYMBOL","GENENAME"))

+  

+  S=res$SYMBOL

 	S[is.na(S)] = ""

-	

-	dmap = .getMapFromOrg(organism, "GENENAME")

-	D = unlist(AnnotationDbi::mget(x, dmap, ifnotfound = NA))

-	D[is.na(D)] = ""

+  

+  D=res$GENENAME

+  D[is.na(D)] = ""

 	grole = rep("bridge", length(x))

 	grole[x %in% query] = "enriched"