@@ -1,8 +1,8 @@

 Package: MotifDb

 Type: Package

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

-Version: 1.5.0

-Date: 2013-08-30

+Version: 1.5.1

+Date: 2014-02-03

 Author: Paul Shannon

 Maintainer: Paul Shannon <pshannon@fhcrc.org>

 Depends: R (>= 2.15.0), methods, IRanges, Biostrings

@@ -204,11 +204,11 @@ setMethod('show', 'MotifList',

       cat ('| Created from downloaded public sources: 2013-Aug-30', '\n', sep='')

-      tbl.dataSource = as.data.frame (table (values (object)$dataSource))

-      tbl.org = as.data.frame (table (values (object)$organism))

+      tbl.dataSource = as.data.frame (table (mcols (object)$dataSource))

+      tbl.org = as.data.frame (table (mcols (object)$organism))

       tbl.org = head (tbl.org [order (tbl.org$Freq, decreasing=TRUE),])

       totalMatrixCount = length (object)

-      totalOrganismCount = length (unique (values (object)$organism))

+      totalOrganismCount = length (unique (mcols (object)$organism))

       dataSourceCount = nrow (tbl.dataSource)

       source.singular.or.plural = 'sources'

@@ -255,9 +255,9 @@ setMethod('show', 'MotifList',

 setMethod ('query', 'MotifList',

    function (object, queryString, ignore.case=TRUE) {

-       indices = unique (as.integer (unlist (sapply (colnames (values (object)), 

+       indices = unique (as.integer (unlist (sapply (colnames (mcols (object)), 

                     function (colname) 

-                       grep (queryString, values (object)[, colname], 

+                       grep (queryString, mcols (object)[, colname], 

                              ignore.case=ignore.case)))))

         object [indices]

       })

@@ -112,7 +112,7 @@ test.noNAorganisms = function ()

 {

   print ('--- test.noNAorganisms')

-  checkEquals (which (is.na (values (MotifDb)$organism)), integer (0))

+  checkEquals (which (is.na (mcols(MotifDb)$organism)), integer (0))

 } # test.noNAorganisms

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

@@ -131,7 +131,7 @@ test.providerNames = function ()

 {

   print ('--- test.getProviderNames')

   mdb = MotifDb # ()

-  pn = values (mdb)$providerName

+  pn = mcols(mdb)$providerName

   checkEquals (length (which (is.na (pn))), 0)

   checkEquals (length (which (pn == '')), 0)

@@ -141,7 +141,7 @@ test.geneSymbols = function ()

 {

   print ('--- test.getGeneSymbols')

   mdb = MotifDb # ()

-  syms = values (mdb)$geneSymbol

+  syms = mcols(mdb)$geneSymbol

   checkEquals (length (which (is.na (syms))), 683)  # no symols yet for the dgf stamlab motifs

   checkEquals (length (which (syms == '')), 0)

@@ -151,8 +151,8 @@ test.geneIdsAndTypes = function ()

 {

   print ('--- test.getGeneIdsAndTypes')

   mdb = MotifDb

-  geneIds = values (mdb)$geneId

-  geneIdTypes = values (mdb)$geneIdType

+  geneIds = mcols(mdb)$geneId

+  geneIdTypes = mcols(mdb)$geneIdType

   typeCounts = as.list (table (geneIdTypes))

   checkEquals(typeCounts, list(ENTREZ=2197, FLYBASE=30, SGD=453, comment=683))

@@ -170,10 +170,10 @@ test.proteinIds = function ()

 {

   print ('--- test.proteinIds')

   mdb = MotifDb # (quiet=TRUE)

-  NA.string.count = length (grep ('NA', values (mdb)$proteinId))

+  NA.string.count = length (grep ('NA', mcols(mdb)$proteinId))

   checkEquals (NA.string.count, 0)

-  empty.count = length (which (values (mdb)$proteinId==""))

+  empty.count = length (which (mcols(mdb)$proteinId==""))

   if (empty.count > 0)

     browser ('test.proteinIds')     

@@ -183,7 +183,7 @@ test.proteinIds = function ()

      # Herve' pointed out that this applied also to entries with no proteinId.

      # make sure this is fixed

-  x = values (mdb)

+  x = mcols(mdb)

   checkEquals (nrow (subset (x, !is.na (proteinIdType) & is.na (proteinId))), 0)

 } # test.proteinIds

@@ -193,7 +193,7 @@ test.sequenceCount = function ()

 {

   print ('--- test.sequenceCount')

   mdb = MotifDb # ()

-  x = values (mdb)

+  x = mcols(mdb)

   if (interactive ()) {

     x.up = subset (x, dataSource == 'UniPROBE')

     checkTrue (all (is.na (x.up$sequenceCount)))

@@ -216,8 +216,8 @@ test.longNames = function ()

   dataSources = unique (sapply (longNames, '[', 2))

-  recognized.dataSources = unique (values (mdb)$dataSource)

-  recognized.organisms = unique (values (mdb)$organism)

+  recognized.dataSources = unique (mcols(mdb)$dataSource)

+  recognized.organisms = unique (mcols(mdb)$organism)

     # a few (3) matrices from JASPAR core have NA organism.  make this into a character

     # so that it can be matched up against the 'NA' extracted from longNames just above

   na.indices = which (is.na (recognized.organisms))

@@ -234,14 +234,14 @@ test.organisms = function ()

 {

   print ('--- test.organisms')

   mdb = MotifDb # (quiet=TRUE)

-  organisms = values (mdb)$organism

+  organisms = mcols(mdb)$organism

      # jaspar_core has 3 NA speciesId: TBP, HNF4A and CEBPA (MA0108.2, MA0114.1, MA0102.2)

      # their website shows these as vertebrates, which I map to 'Vertebrata'.  An organismID of '-'

      # gets the same treatment, matching website also.

-  checkEquals (which (is.na (values (MotifDb)$organism)), integer (0))

+  checkEquals (which (is.na (mcols(MotifDb)$organism)), integer (0))

-  empty.count = length (which (values (mdb)$organism==""))

+  empty.count = length (which (mcols(mdb)$organism==""))

   checkEquals (empty.count, 0)

 } # test.organisms

@@ -250,7 +250,7 @@ test.bindingDomains = function ()

 {

   print ('--- test.bindingDomains')

   mdb = MotifDb # (quiet=TRUE)

-  checkTrue (length (unique (values (mdb)$bindingDomain)) > 1)

+  checkTrue (length (unique (mcols(mdb)$bindingDomain)) > 1)

 } # test.bindingDomains

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

@@ -258,7 +258,7 @@ test.flyBindingDomains = function ()

 {

   print ('--- test.flyBindingDomains')

-  x = values (MotifDb)

+  x = mcols(MotifDb)

   tmp = as.list (head (sort (table (subset (x, organism=='Dmelanogaster')$bindingDomain), decreasing=TRUE), n=3))

     # these counts will likely change with a fresh load of data from FlyFactorSurvey.

@@ -274,7 +274,7 @@ test.experimentTypes = function ()

 {

   print ('--- test.experimentTypes')

   mdb = MotifDb # (quiet=TRUE)

-  x = values (mdb)

+  x = mcols(mdb)

   checkTrue (length (unique (x$experimentType)) >= 18)

   checkEquals (length (which (x$experimentType=='')), 0)

@@ -284,7 +284,7 @@ test.tfFamilies = function ()

 {

   print ('--- test.tfFamilies')

   mdb = MotifDb # (quiet=TRUE)

-  checkTrue (length (unique (values (mdb)$tfFamily)) > 1)

+  checkTrue (length (unique (mcols(mdb)$tfFamily)) > 1)

 } # test.tfFamilies

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

@@ -292,14 +292,14 @@ test.bindingSequences = function ()

 {

   print ('--- test.bindingSequences')

   mdb = MotifDb # (quiet=TRUE)

-  checkTrue (length (unique (values (mdb)$bindingSequence)) > 1)

+  checkTrue (length (unique (mcols(mdb)$bindingSequence)) > 1)

 } # test.tfFamilies

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

 test.pubmedIDs = function ()

 {

   print ('--- test.pubmedIDs')

-  x = values (MotifDb) # (quiet=TRUE))

+  x = mcols(MotifDb) # (quiet=TRUE))

   checkTrue (length (unique (x$pubmedID)) >= 139)

   checkEquals (length (which (x$pubmedID == '')), 0)

@@ -323,7 +323,7 @@ test.allFullNames = function ()

   matrices = mdb@listData

   fullNames = names (matrices)

-  all.dataSources = unique (values (mdb)$dataSource)

+  all.dataSources = unique (mcols(mdb)$dataSource)

   checkTrue (length (all.dataSources) >= 4)

   for (source in all.dataSources) {

@@ -374,7 +374,7 @@ test.query = function ()

   mdb = MotifDb

     # do queries on dataSource counts match those from a contingency table?

-  sources.list = as.list (table (values (mdb)$dataSource))

+  sources.list = as.list (table (mcols(mdb)$dataSource))

   checkEquals (length (query (mdb, 'flyfactorsurvey')), sources.list$FlyFactorSurvey)

   checkEquals (length (query (mdb, 'uniprobe')), sources.list$UniPROBE)

   checkEquals (length (query (mdb, 'UniPROBE')), sources.list$UniPROBE)

@@ -399,9 +399,9 @@ test.query = function ()

   checkTrue (length (uniprobe.sox.matrices) > 10)

   checkTrue (length (uniprobe.sox.matrices) < 30)

-   checkEquals (unique (values (uniprobe.sox.matrices)$dataSource), 'UniPROBE')

-   checkEquals (unique (values (sox.uniprobe.matrices)$dataSource), 'UniPROBE')

-   gene.symbols = sort (unique (values (uniprobe.sox.matrices)$geneSymbol))

+   checkEquals (unique (mcols(uniprobe.sox.matrices)$dataSource), 'UniPROBE')

+   checkEquals (unique (mcols(sox.uniprobe.matrices)$dataSource), 'UniPROBE')

+   gene.symbols = sort (unique (mcols(uniprobe.sox.matrices)$geneSymbol))

 } # test.query

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