@@ -1,11 +1,11 @@

 Package: MotifDb

 Type: Package

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

-Version: 1.23.8

+Version: 1.23.9

 Date: 2018-05-23

 Author: Paul Shannon, Matt Richards

 Maintainer: Paul Shannon <pshannon@systemsbiology.org>

-Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings

+Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings, motifStack

 Suggests: RUnit, seqLogo, MotIV

 Imports: rtracklayer, splitstackshape

 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.

@@ -491,7 +491,7 @@ setMethod ('geneToMotif', 'MotifList',

    function (object, geneSymbols, source, ignore.case=FALSE) {

      source <- tolower(source)

-     stopifnot(source %in% c("motifdb", "tfclass"))

+     stopifnot(all(source %in% c("motifdb", "tfclass")))

      extract.mdb <- function(gene){

         geneSymbol <- NULL # workaround the R CMD check "no visible binding for global variable"

         if(ignore.case)

@@ -503,13 +503,13 @@ setMethod ('geneToMotif', 'MotifList',

         colnames(tbl) <- c("geneSymbol", "motif", "dataSource", "organism", "pubmedID")

         tbl

         }

-     if(source %in% c("motifdb")){

+     if("motifdb" %in% source){

         tbls <- lapply(geneSymbols, extract.mdb)

         result <- do.call(rbind, tbls)

         if(nrow(result) > 0)

            result$source <- "MotifDb"

         }

-     if(source %in% c("tfclass")){

+     if("tfclass" %in% source){

         if(ignore.case)

            tbl <- subset(object@manuallyCuratedGeneMotifAssociationTable, tolower(tf.gene) %in% tolower(geneSymbols))

         else

new file mode 100644

@@ -0,0 +1,15 @@

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

+plotMotifs <- function(motifs)

+{

+   stopifnot(length(motifs) > 0)

+

+  if(length(motifs) == 1){

+    pcm <- new("pcm", mat=motifs[[1]], name=names(motifs))

+    plot(pcm)

+    }

+

+  motifStack(lapply(names(motifs), function(mName) new("pfm", motifs[[mName]], name=mName)))

+

+} # plotMotifs

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

+

@@ -1070,3 +1070,5 @@ findMotifsWithMutuallyExclusiveMappings <- function()

 } # findMotifsWithMutuallyExclusiveMappings

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

+if(!interactive())

+   runTests()