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

 Package: MotifDb

 Type: Package

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

-Version: 1.19.20

+Version: 1.19.22

 Date: 2018-01-23

 Author: Paul Shannon, Matt Richards

 Maintainer: Paul Shannon <pshannon@systemsbiology.org>

@@ -7,7 +7,7 @@ strands: + -

 Background letter frequencies

 A 0.250 C 0.250 G 0.250 T 0.250 

-MOTIF Mmusculus-cispb_1.02-M0082_1.02

+MOTIF Mmusculus-cisbp_1.02-M0082_1.02

 letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020

  0.2203768432  0.3354050831  0.1020373584  0.3421807153

  0.1117838556  0.1937497051  0.6695240896  0.0249423496

@@ -20,7 +20,7 @@ letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020

  0.0551007724  0.0004313497  0.9430919013  0.0013759766

  0.0952369898  0.3494527694  0.4354449644  0.1198652764

-MOTIF Mmusculus-cispb_1.02-M0083_1.02

+MOTIF Mmusculus-cisbp_1.02-M0083_1.02

 letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020

  0.1631992133  0.1296672588  0.1083071987  0.5988263292

  0.2034461212  0.3491149401  0.2460171402  0.2014217985

@@ -33,7 +33,7 @@ letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020

  0.1006336198  0.0000926882  0.8991828391  0.0000908529

  0.0001197413  0.0000375373  0.9998233202  0.0000194012

-MOTIF Mmusculus-cispb_1.02-M0084_1.02

+MOTIF Mmusculus-cisbp_1.02-M0084_1.02

 letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020

  0.1947249309  0.4000493650  0.1501429668  0.2550827372

  0.0896002212  0.3254984788  0.5260297596  0.0588715404

deleted file mode 100644

@@ -1,221 +0,0 @@

-library (MotifDb)

-library (RUnit)

-library (MotIV)

-library (seqLogo)

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

-printf <- function(...) print(noquote(sprintf(...)))

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

-# Note: all matrix numbers were chosen randomly using "sample()"

-runTests = function ()

-{

-

-} # runTests

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

-test_cisbp <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/cisbp_matrix.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_cisbp

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

-test_FlyFactorSurvey <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/FlyFactorSurvey.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_FlyFactorSurvey

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

-test_HOCOMOCOv10 <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/HOCOMOCOv10.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_HOCOMOCOv10

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

-test_HOMER <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/HOMER.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_HOMER

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

-test_hPDI <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/hPDI.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_hPDI

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

-test_JASPAR_2014 <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/JASPAR_2014.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_JASPAR_2014

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

-test_JASPAR_CORE<- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/JASPAR_CORE.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_JASPAR_CORE

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

-test_jaspar2016 <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/jaspar2016.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_jaspar2016

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

-test_jolma2013 <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/jolma2013.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_jolma2013

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

-test_ScerTF <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/ScerTF.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_ScerTF

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

-test_stamlab <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/stamlab.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_stamlab

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

-test_SwissRegulon <- function(){

-

-    # Load the cisbp matrix as "cisbp"

-    load("./single_matrices/SR_matrix.Rdata")

-    

-    # Matrix name

-    mtx.name <- "M0308_1.02"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(cisbp == queried))

-    

-} # test_SwissRegulon

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

-test_UniPROBE <- function(){

-

-    # Load the uniprobe matrix as "uniprobe"

-    load("./single_matrices/UniPROBE_matrix.Rdata")

-    

-    # Matrix name

-    mtx.name <- "UP00230"

-

-    # Query for the same matrix

-    queried <- query(MotifDb, mtx.name)[[1]]

-

-    # Check that they're the same

-    checkTrue(all(uniprobe == queried))

-    

-} # test_UniPROBE

-

@@ -42,9 +42,10 @@ runTests = function ()

   test.export_jasparFormatToFile()

   test.geneToMotif()

+  test.geneToMotif.ignore.jasparSuffixes()

   test.motifToGene()

-  test.associateTranscriptionFactors()

+  test.associateTranscriptionFactors()

 } # runTests

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

 test.emptyCtor = function ()

@@ -288,10 +289,10 @@ test.flyBindingDomains = function ()

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

-  checkEquals (tmp$Homeobox, 212)

-  checkEquals (tmp[['zf-C2H2']], 160)

-  checkEquals (tmp[["Helix-Turn-Helix"]], 182)

-  checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 301) # lots of cisbp

+  checkEquals(tmp$Homeobox, 212)

+  checkEquals(tmp[['zf-C2H2']], 160)

+  checkEquals(tmp[["Helix-Turn-Helix"]], 182)

+  checkTrue(length(which(is.na(subset(x, organism=='Dmelanogaster')$bindingDomain))) > 300) # lots of cisbp

 } # test.flyBindingDomains

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

@@ -563,7 +564,7 @@ test.export_memeFormatToFileDuplication = function ()

   print ('--- test.export_memeFormatToFileDuplication')

   mdb = MotifDb # ()

   mdb.mouse = subset (mdb, organism=='Mmusculus')

-  checkEquals (length (mdb.mouse), 1251)

+  checkTrue(length(mdb.mouse) > 1300)

   output.file = 'mouse.txt' # tempfile ()

   max = 3

   meme.text = export (mdb.mouse [1:max], output.file, 'meme')

@@ -771,7 +772,7 @@ test.geneToMotif <- function()

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

    tbl.mdb <- geneToMotif(mdb, genes, source="mOtifdb")     # intentional mis-capitalization

-   checkEquals(dim(tbl.mdb), c(12, 6))

+   checkEquals(dim(tbl.mdb), c(13, 6))

    checkEquals(subset(tbl.mdb, dataSource=="jaspar2016" & geneSymbol== "FOS")$motif, "MA0476.1")

       # no recognizable (i.e., jaspar standard) motif name returned by MotifDb metadata

       # MotifDb for ATF5

@@ -809,9 +810,11 @@ test.geneToMotif.ignore.jasparSuffixes <- function()

       # this establishes the need for careful scrutiny as one winnows a geneToMotif result into

       # useful non-reduplicative sequence analysis

-   checkEquals(as.list(query(mdb, "MA0110599")), as.list(query(query(mdb, "MA0476.1"), "jaspar2018")))

+   pfm.ma0110599 <- as.list(query(mdb, "MA0110599"))[[1]]

+   pfm.ma0476.1  <- as.list(query(query(mdb, "MA0476.1"), "jaspar2018"))[[1]]

+   checkEquals(pfm.ma0110599, pfm.ma0476.1)

-} # test.geneToMotif

+} # test.geneToMotif.ignore.jasparSuffixes

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

 test.motifToGene <- function()

 {

@@ -822,14 +825,15 @@ test.motifToGene <- function()

       # MotifDb mode uses the MotifDb metadata "providerId",

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

-   checkEquals(dim(tbl.mdb), c(3, 6))

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

+   checkEquals(dim(tbl.mdb), c(4, 6))

+   expected <- sort(c("MA0592.2", "MA0592.2", "ELF1.SwissRegulon", "UP00022"))

    actual <- sort(tbl.mdb$motif)

    checkEquals(actual, expected)

-   checkEquals(sort(tbl.mdb$geneSymbol), sort(c("Esrra", "ELF1", "Zfp740")))

-   checkEquals(sort(tbl.mdb$dataSource), sort(c("jaspar2016", "SwissRegulon", "UniPROBE")))

-   checkEquals(sort(tbl.mdb$organism),   sort(c("Mmusculus", "Hsapiens", "Mmusculus")))

-   checkEquals(sort(tbl.mdb$source),     rep("MotifDb", 3))

+   checkEquals(sort(tbl.mdb$geneSymbol), sort(c("ELF1", "Esrra", "Esrra", "Zfp740")))

+   checkEquals(sort(tbl.mdb$dataSource), sort(c("jaspar2016", "jaspar2018", "SwissRegulon", "UniPROBE")))

+

+   checkEquals(sort(tbl.mdb$organism),   sort(c("Hsapiens", "Mmusculus", "Mmusculus", "Mmusculus")))

+   checkEquals(tbl.mdb$source,     rep("MotifDb", 4))

       # TFClass mode uses  TF family classifcation

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