@@ -1,12 +1,13 @@

 Package: CNEr 

-Version: 1.13.0

-Date: 2017-04-10

+Version: 1.13.1

+Date: 2017-07-03

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

 Author: Ge Tan <ge_tan@live.com>

 Maintainer: Ge Tan <ge_tan@live.com>

 Imports: Biostrings (>= 2.33.4),

+         DBI (>= 0.7),

          RSQLite (>= 0.11.4),

          GenomeInfoDb (>= 1.1.3),

          GenomicRanges (>= 1.23.16),

@@ -27,7 +28,7 @@ Imports: Biostrings (>= 2.33.4),

          GO.db (>= 3.3.0),

          R.utils (>= 2.3.0),

          KEGGREST (>= 1.14.0)

-Depends: R (>= 3.2.2)

+Depends: R (>= 3.4)

 Suggests: Gviz (>= 1.7.4),

           BiocStyle,

           knitr,

@@ -19,7 +19,8 @@ importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,

 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,

                                  findOverlaps, coverage, grglist)

 importMethodsFrom(XVector, subseq)

-importMethodsFrom(RSQLite, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)

+importMethodsFrom(DBI, dbGetQuery)

+importMethodsFrom(RSQLite, dbConnect, dbDisconnect, dbWriteTable)

 importMethodsFrom(methods, initialize, show)

 importMethodsFrom(Biostrings, compareStrings)

 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,

@@ -156,7 +157,7 @@ export(

   plotCNEWidth, plotCNEDistribution,

   # GO.R

-  addAncestorGO,

+  ## addAncestorGO,

   ## AssemblyStats.R

   N50, N90

@@ -138,9 +138,10 @@ addAncestorGO <- function(go){

   }

   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)

+  allGo <- unlist(go)

+  goID2Ancestor <- lapply(goID2Ancestor, function(x){x[x%in%allGo]})

+  newGo <- lapply(relist(mapply(append, allGo, goID2Ancestor[allGo]), go),

+                  unlist)

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

   return(newGo)

 }

new file mode 100644

@@ -0,0 +1,39 @@

+\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{

+  \donttest{

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

+})

\ No newline at end of file