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

 Package: CNEr 

-Version: 1.9.42

-Date: 2016-10-04

+Version: 1.9.43

+Date: 2016-10-06

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

@@ -86,8 +86,7 @@ readAncoraIntoSQLite <- function(cneFns, dbName, overwrite=FALSE){

 ### -----------------------------------------------------------------

 ### makeCNEDensity: make the Ancora downloads-like bed files, bedgraph, 

-### bigwig files

-###   from a GrangePairs of CNEs.

+### bigwig files from a GrangePairs of CNEs.

 ### Exported!

 makeCNEDensity <- function(x, outputDir=".",

                            genomeFirst="first", genomeSecond="second",

@@ -56,6 +56,7 @@

   \code{\link{readAncora}}

 }

 \examples{

+  \dontrun{

   dbName <- file.path(system.file("extdata", package="CNEr"),

                       "danRer10CNE.sqlite")

   qAssemblyFn <- file.path(system.file("extdata",

@@ -64,9 +65,10 @@

   tAssemblyFn <- file.path(system.file("extdata",

                              package="BSgenome.Drerio.UCSC.danRer10"),

                            "single_sequences.2bit")

-  cneGRangePairs <- readCNERangesFromSQLite(dbName=dbName, 

+  cneGRangePairs <- readCNERangesFromSQLite(dbName=dbName,

                                             tableName="danRer10_hg38_45_50",

                                             tAssemblyFn=tAssemblyFn,

                                             qAssemblyFn=qAssemblyFn)

   makeCNEDensity(cneGRangePairs[1:1000])

+  }

 }

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