@@ -1,6 +1,6 @@

 Package: CNEr 

-Version: 1.11.7

-Date: 2017-02-23

+Version: 1.11.8

+Date: 2017-04-10

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

@@ -155,6 +155,9 @@ export(

   # CNE-utils.R

   plotCNEWidth, plotCNEDistribution,

+  # GO.R

+  addAncestorGO,

+  

   ## AssemblyStats.R

   N50, N90

 )

@@ -4,6 +4,7 @@ NEW FEATURES

     o Add function orgKEGGIds2EntrezIDs to fetch the mapping between KEGG IDs

       and Entrez IDs

     o Add function makeAxtTracks

+    o Add function addAncestorGO

 CHANGES IN Bioc 3.4

 ------------------------

@@ -127,4 +127,20 @@ readGAF <- function(fn){

   GOTerms <- sapply(strsplit(lines, "\t"), "[", 5)

   ans <- split(GOTerms, geneIDs)

   return(ans)

-}

\ No newline at end of file

+}

+

+### -----------------------------------------------------------------

+### Add ancestor GO

+### Exported!

+addAncestorGO <- function(go){

+  if(!is(go, "list")){

+    stop("`go` must be a list!")

+  }

+  goID2Ancestor <- c(as.list(GOBPANCESTOR), as.list(GOMFANCESTOR), 

+                     as.list(GOCCANCESTOR))

+  newGo <- lapply(relist(lapply(mapply(append, unlist(go), 

+                                       goID2Ancestor[unlist(go)]), 

+                                function(x){x[x!="all"]}), go), unlist)

+  newGo <- lapply(newGo, function(x){if(is.null(x)){character(0)}else{x}})

+  return(newGo)

+}

new file mode 100644

@@ -0,0 +1,37 @@

+\name{addAncestorGO}

+\alias{addAncestorGO}

+\title{

+  Add ancestor GO IDs

+}

+\description{

+  Given a list of GO IDs, add the corresponding ancestor GO IDs.

+}

+\usage{

+  addAncestorGO(go)

+}

+\arguments{

+  \item{go}{

+    A \code{list} of GO IDs. The elements of the list can be empty.

+  }

+}

+\details{

+  The ancestor GO IDs for each GO ID are added to the elements.

+}

+\value{

+  A \code{list} of GO IDs with their ancestor GO IDs.

+}

+\author{

+  Ge Tan

+}

+\note{

+  This function is mainly designed for processing the gff annotation generated

+  from interproscan, where for each gene, a set of GO IDs are assigned.

+  However, for GO enrichment analysis, we need a list of mapping from genes to

+  the GO IDs and their ancestor GO IDs as well.

+}

+

+\examples{

+  library(GO.db)

+  go <- list(c("GO:0005215", "GO:0006810", "GO:0016020"), "GO:0016579")

+  addAncestorGO(go)

+}

new file mode 100644

@@ -0,0 +1,6 @@

+test_that("test_addAncestorGO", {

+  library(GO.db)

+  go <- list(c("GO:0005215", "GO:0006810", "GO:0016020"), "GO:0016579")

+  newGO <- addAncestorGO(go)

+  expect_identical(lengths(newGO), c(8, 17))

+})

\ No newline at end of file