@@ -2,8 +2,15 @@ annotate.genes <- function(keys, annotation.db, keytype = "ENTREZID",

     columns = list(EntrezId = "ENTREZID", Symbol = "SYMBOL", 

         GeneName = "GENENAME"))

 {

-    if(class(annotation.db) == "character")

-        annotation.db <- get(annPkgName(annotation.db))

+    if(class(annotation.db) == "character"){

+        if(exists(annPkgName(annotation.db, "db"))){

+            annotation.db <- get(annPkgName(annotation.db, "db"))

+        } else if(exists(annPkgName(annotation.db, "env"))){

+            annotation.db <- get(annPkgName(annotation.db, "env"))

+        } else{

+            stop("Can't find annotation database:", annotation.db)

+        }

+    }

     ## For each column, return the values for the keys of interest

     ## using the keys and keytype provided above.

@@ -2,6 +2,7 @@

 ##' 

 ##' @param ids character vector containing gene identifiers

 ##' @param annotation.db character string containing annotation database that matches with gene identifiers

+##' @param keytype character string containing what kind of keys were passed in.

 check.eg.ids <- function(ids, annotation.db = 'org.Hs.eg'){

     ann.map <- getAnnMap("SYMBOL", annotation.db)

     check <- unlist(mget(ids, ann.map, ifnotfound=NA))

@@ -13,6 +14,16 @@ check.eg.ids <- function(ids, annotation.db = 'org.Hs.eg'){

 }

 check.ids <- function(ids, annotation.db = org.Hs.eg.db, keytype = "ENTREZID"){

+    if(class(annotation.db) == "character"){

+        if(exists(annPkgName(annotation.db, "db"))){

+            annotation.db <- get(annPkgName(annotation.db, "db"))

+        } else if(exists(annPkgName(annotation.db, "env"))){

+            annotation.db <- get(annPkgName(annotation.db, "env"))

+        } else{

+            stop("Can't find annotation database:", annotation.db)

+        }

+    }

+    

     allIds <- keys(annotation.db, keytype = keytype)

     check <- sum(ids %in% allIds)

     if(check == 0){

@@ -77,7 +77,8 @@ setMethod("toReportDF",

     signature = signature(object = "DESeqResults"),

     definition = function(object, htmlReport, DataSet = NULL, 

         annotation.db = NULL, pvalueCutoff = 0.01, lfc = 0, n = 500,

-        sort.by = "pvalue", make.plots = FALSE, ..., name = NULL)

+        sort.by = "pvalue", make.plots = FALSE, keytype = "ENTREZID", ..., 

+        name = NULL)

     {

         resTab <- as.data.frame(object[

             which(object$padj < pvalueCutoff & 

@@ -93,15 +94,17 @@ setMethod("toReportDF",

         if(n < nrow(resTab))

             resTab <- resTab[1:n, ]

-        ann.map.available <- tryCatch(getAnnMap("SYMBOL", annotation.db), 

-            error=function(e){ return(FALSE) })

+        ann.db.available <- !is.null(annotation.db) && 

+            (exists(annPkgName(annotation.db, "db")) || 

+                exists(annPkgName(annotation.db, "env")))

-        if (inherits(ann.map.available, "AnnDbBimap")){

+        if (ann.db.available){

             ## Check valid Entrez ids are passed in

-            check.eg.ids(rownames(resTab), annotation.db)

+            check.ids(rownames(resTab), annotation.db, keytype = keytype)

-            fdata <- ReportingTools:::annotate.genes(rownames(resTab), annotation.db,

-                keytype = "ENTREZID", columns = list(EntrezId = "ENTREZID", 

+            fdata <- ReportingTools:::annotate.genes(rownames(resTab), 

+                annotation.db, keytype = keytype, 

+                columns = list(EntrezId = "ENTREZID", 

                     Symbol = "SYMBOL", GeneName = "GENENAME"))

         } else {

             fdata <- data.frame(ID = rownames(resTab), stringsAsFactors = FALSE)

@@ -138,7 +141,7 @@ setMethod("toReportDF",

     definition = function(object, htmlReport, 

         contrast = NULL, resultName = NULL, annotation.db = NULL,

         pvalueCutoff = 0.01, lfc = 0, n = 500, sort.by = "pvalue", 

-        make.plots = FALSE, ...)

+        make.plots = FALSE, keytype = "ENTREZID", ...)

     {

         if (!"results" %in% mcols(mcols(object))$type) {

             stop("No results found in DESeqDataSet, please run DESeq first.")

@@ -159,15 +162,16 @@ setMethod("toReportDF",

         if(n < nrow(resTab))

             resTab <- resTab[1:n, ]

-        ann.map.available <- tryCatch(getAnnMap("SYMBOL", annotation.db), 

-            error=function(e){ return(FALSE) })

-

-        if (inherits(ann.map.available, "AnnDbBimap")){

+        ann.db.available <- !is.null(annotation.db) && 

+            (exists(annPkgName(annotation.db, "db")) || 

+                exists(annPkgName(annotation.db, "env")))

+                

+        if (ann.db.available){

             ## Check valid Entrez ids are passed in

-            check.eg.ids(rownames(resTab), annotation.db)

+            check.ids(rownames(resTab), annotation.db, keytype = keytype)

             fdata <- annotate.genes(rownames(resTab), annotation.db,

-                keytype = "ENTREZID", columns = list(EntrezId = "ENTREZID", 

+                keytype = keytype, columns = list(EntrezId = "ENTREZID", 

                     Symbol = "SYMBOL", GeneName = "GENENAME"))

         } else {

             fdata <- data.frame(ID = rownames(resTab), stringsAsFactors = FALSE)

@@ -25,4 +25,5 @@ test_AnnotationData <- function()

         "NA is returned for keys that have 1:many relationships")

     checkTrue(sum(ann.vals[,"Symbol"] == "B2M") == 2,

         "2 rows are returned for a duplicated key")

-}

\ No newline at end of file

+}

+