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

 Package: MotifDb

 Type: Package

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

-Version: 1.19.10

+Version: 1.19.11

 Date: 2017-10-03

 Author: Paul Shannon, Matt Richards

 Maintainer: Paul Shannon <pshannon@systemsbiology.org>

@@ -353,14 +353,17 @@ setMethod ('motifToGene', 'MotifList',

      tbl <- data.frame()

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

         tbl <- as.data.frame(subset(mcols(object), providerId %in% motifs))

+        if(nrow(tbl) == 0)

+           return(data.frame())

         tbl <- unique(tbl [, c("geneSymbol", "providerId", "dataSource", "organism", "pubmedID")])

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

-        tbl

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

         tbl$from <- "MotifDb"

         }

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

         tbl <- subset(object@manuallyCuratedGeneMotifAssociationTable, motif %in% motifs)

+        if(nrow(tbl) == 0)

+           return(data.frame())

         tbl <- unique(tbl[, c("motif", "tf.gene", "pubmedID")])

         tbl <- tbl[order(tbl$motif),]

         rownames(tbl) <- NULL

@@ -424,9 +427,11 @@ setMethod('associateTranscriptionFactors', 'MotifList',

            }

         tbl.tfClass <- read.table(system.file(package="MotifDb", "extdata", "tfClass.tsv"), sep="\t", as.is=TRUE, header=TRUE)

         motif.ids <- tbl.withMotifs[, "shortMotif"]

-        geneSymbols <- lapply(motif.ids, function(id) paste(tbl.tfClass$tf.gene[grep(id, tbl.tfClass$motif)], collapse=";"))

+        geneSymbols <- lapply(motif.ids, function(id)

+                                 paste(tbl.tfClass$tf.gene[grep(id, tbl.tfClass$motif, fixed=TRUE)], collapse=";"))

         geneSymbols <- unlist(geneSymbols)

-        pubmedIds   <- lapply(motif.ids, function(id) unique(tbl.tfClass$pubmedID[grep(id, tbl.tfClass$motif)]))

+        pubmedIds   <- lapply(motif.ids, function(id)

+                                 unique(tbl.tfClass$pubmedID[grep(id, tbl.tfClass$motif, fixed=TRUE)]))

         pubmedIds   <- as.character(pubmedIds)

         pubmedIds   <- gsub("integer(0)", "", pubmedIds, fixed=TRUE)

         tbl.new     <- data.frame(geneSymbol=geneSymbols, pubmedID=pubmedIds, stringsAsFactors=FALSE)

@@ -772,19 +772,19 @@ test.geneToMotif <- function()

       # MotifDb for ATF5

       # todo: compare the MA0110596_1.02 matrix of cisp_1.02 to japar MA0833.1

-    # now try motifs to genes

-

 } # test.geneToMotif

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

 test.motifToGene <- function()

 {

    printf("--- test.motifToGene")

-   mdb <- MotifDb

    motifs <- c("MA0592.2", "UP00022", "ELF1.SwissRegulon")

-      # TFClass mode uses  TF family classifcation

-   tbl.d <- motifToGene(mdb, motifs, source="MotifDb")

+   set.seed(31);

+   motifs.long <- names(MotifDb)[sample(1:length(MotifDb), 10)]

+

+      # MotifDb mode uses the MotifDb metadata, pulled from many sources

+   tbl.d <- motifToGene(MotifDb, motifs, source="MotifDb")

    checkEquals(dim(tbl.d), c(3, 6))

    checkEquals(tbl.d$motif, c("MA0592.2", "ELF1.SwissRegulon", "UP00022"))

    checkEquals(tbl.d$geneSymbol, c("Esrra", "ELF1", "Zfp740"))

@@ -792,14 +792,26 @@ test.motifToGene <- function()

    checkEquals(tbl.d$organism,   c("Mmusculus", "Hsapiens", "Mmusculus"))

    checkEquals(tbl.d$from,       rep("MotifDb", 3))

-      # MotifDb mode uses the MotifDb metadata, pulled from many sources

-   tbl.i <- motifToGene(mdb, motifs, source="TFClass")

+

+      # TFClass mode uses  TF family classifcation

+   tbl.i <- motifToGene(MotifDb, motifs, source="TFClass")

    checkEquals(dim(tbl.i), c(9,4))

    checkEquals(tbl.i$motif, rep("MA0592.2", 9))

    checkEquals(sort(tbl.i$gene), c("AR", "ESR1", "ESR2", "ESRRA", "ESRRB", "ESRRG", "NR3C1", "NR3C2", "PGR"))

    checkEquals(tbl.i$from,       rep("TFClass", 9))

-} # test.geneToMotif

+     # test motifs with regex characters in them, or other characters neither letter nor number

+   motifs <- sort(c("DMAP1_NCOR{1,2}_SMARC.p2", "ELK1,4_GABP{A,B1}.p3", "SNAI1..3.p2", "EWSR1-FLI1.p2", "ETS1,2.p2"))

+   tbl <- motifToGene(MotifDb, motifs, source="MotifDb")

+   checkEquals(nrow(tbl), 0)

+

+   tbl <- motifToGene(MotifDb, motifs, source="tfclass")

+   checkEquals(ncol(tbl), 4)

+   checkTrue(nrow(tbl) > 80)

+   checkTrue(nrow(tbl) < 100)

+   checkTrue(all(motifs %in% tbl$motif))

+

+} # test.motifToGene

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

 test.associateTranscriptionFactors <- function()

 {