@@ -1,7 +1,7 @@

 Package: MotifDb

 Type: Package

 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs

-Version: 1.3.7

+Version: 1.3.8

 Date: 2013-04-09

 Author: Paul Shannon

 Maintainer: Paul Shannon <pshannon@fhcrc.org>

@@ -35,7 +35,7 @@ run.tests = function ()

   test.export_memeFormatToFile_run_tomtom ()

   test.run_MotIV ()

   test.MotIV.toTable ()

-  

+  test.flyFactorGeneSymbols()

 } # run.tests

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

@@ -644,5 +644,47 @@ pwmMatch.toTable = function (motifMatch) {

    }

    names(df.list) <- names(motifMatch)

    return (df.list)

-}

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

+

+} # pwmMatch.toTable

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

+# Robert Stojnic reports incorrect gene symbols for matrices obtained from

+# flyFactorSurvey.

+# the solution was to abandon the original strategy of extracting the

+# symbol from the matrix (and file) name.

+# now, the flybase importer ("inst/scripts/import/flyFactorSurvey/import.R")

+# uses FBgn id (which can be reliably extracted) and uses indpendent

+# data sources to learn the gene symbol.

+#

+# robert's email:

+#  I'm working on using MotifDb motifs in my PWMEnrich package and I

+#  have noticed that there is a slight problem with gene symbols for

+#  Drosophila. In particular, the gene symbols do not always correspond

+#  to the gene ID and are frequently mis-capitalized. In Drosophila z

+#  and Z are two different genes and capitalization does matter if

+#  someone is to use the gene symbols. Also, in some cases the symbols

+#  are missing hyphens or parenthesis. I have used the gene IDs and the

+#  Flybase annotation database to set the correct gene symbols for

+#  Drosophila, please find attached the result of my re-annotation.

+#

+#  looking at his correctedMotifDbDmel.csv 

+#

+#    head(read.table("correctedMotifDbDmel.csv", sep=",", header=TRUE, stringsAsFactors=FALSE))

+#                  providerName oldGeneSymbol newGeneSymbol

+#    1 ab_SANGER_10_FBgn0259750            Ab            ab

+#    2  ab_SOLEXA_5_FBgn0259750            Ab            ab

+#    3 Abd-A_FlyReg_FBgn0000014         Abd-a         abd-A

+#    4 Abd-B_FlyReg_FBgn0000015         Abd-b         Abd-B

+#    5    AbdA_Cell_FBgn0000014          Abda         abd-A

+#    6  AbdA_SOLEXA_FBgn0000014          Abda         abd-A

+#

+test.flyFactorGeneSymbols <- function()

+{

+    print ("--- test.flyFactorGeneSymbols")

+    mdb = MotifDb

+    checkEquals(mcols(query(mdb, "FBgn0259750"))$geneSymbol, c("ab", "ab"))

+    checkEquals(mcols(query(mdb, "FBgn0000014"))$geneSymbol, rep("abd-A", 3))

+    checkEquals(mcols(query(mdb, "FBgn0000015"))$geneSymbol, rep("Abd-B", 3))

+

+} # test.flyFactorGeneSymbols

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

+