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

 Package: MotifDb

 Type: Package

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

-Version: 1.29.3

-Date: 2020-03-16

+Version: 1.29.4

+Date: 2020-03-18

 Author: Paul Shannon, Matt Richards

 Maintainer: Paul Shannon <pshannon@systemsbiology.org>

 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings

Binary files a/inst/extdata/hocomoco11.RData and b/inst/extdata/hocomoco11.RData differ

@@ -1196,19 +1196,19 @@ test.hocomoco11.with.reliabilityScores <- function()

    checkEquals(length(query(MotifDb, "hocomocov10")), 1066)

    checkEquals(length(query(MotifDb, "hocomocov11")), 768)

    checkEquals(length(query(MotifDb, "hocomocov11-core")), 400)

-   checkEquals(length(query(MotifDb, "hocomocov11-full")), 368)

+   checkEquals(length(query(MotifDb, "hocomocov11-secondary")), 368)

    checkEquals(length(query(MotifDb, "hocomocov11-core-A")), 181)

-   checkEquals(length(query(MotifDb, "hocomocov11-full-A")), 46)

+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-A")), 46)

    checkEquals(length(query(MotifDb, "hocomocov11-core-B")), 84)

-   checkEquals(length(query(MotifDb, "hocomocov11-full-B")), 19)

+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-B")), 19)

    checkEquals(length(query(MotifDb, "hocomocov11-core-C")), 135)

-   checkEquals(length(query(MotifDb, "hocomocov11-full-C")), 13)

+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-C")), 13)

    checkEquals(length(query(MotifDb, "hocomocov11-core-D")), 0)

-   checkEquals(length(query(MotifDb, "hocomocov11-full-D")), 290)

+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-D")), 290)

 } # test.hocomoco11.with.reliabilityScores

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

Binary files a/vignettes/MotifDb-egr1.pdf and b/vignettes/MotifDb-egr1.pdf differ

@@ -86,20 +86,24 @@ There are  more than two thousand  matrices, from five sources:

 > length (MotifDb)

 \end{Sinput}

 \begin{Soutput}

-[1] 10333

+[1] 10701

 \end{Soutput}

 \begin{Sinput}

 > sort (table (values (MotifDb)$dataSource), decreasing=TRUE)

 \end{Sinput}

 \begin{Soutput}

-     jaspar2018      jaspar2016     HOCOMOCOv10      cisbp_1.02       jolma2013 

-           1564            1209            1066             874             843 

-   SwissRegulon         stamlab FlyFactorSurvey     JASPAR_2014     JASPAR_CORE 

-            684             683             614             592             459 

-           hPDI        UniPROBE           HOMER          ScerTF    HOCOMOCOv11A 

-            437             380             332             196             181 

-   HOCOMOCOv11C    HOCOMOCOv11B 

-            135              84 

+        jaspar2018         jaspar2016        HOCOMOCOv10         cisbp_1.02 

+              1564               1209               1066                874 

+         jolma2013       SwissRegulon            stamlab    FlyFactorSurvey 

+               843                684                683                614 

+       JASPAR_2014        JASPAR_CORE               hPDI           UniPROBE 

+               592                459                437                380 

+             HOMER HOCOMOCOv11-full-D             ScerTF HOCOMOCOv11-core-A 

+               332                290                196                181 

+HOCOMOCOv11-core-C HOCOMOCOv11-core-B HOCOMOCOv11-full-A HOCOMOCOv11-full-B 

+               135                 84                 46                 19 

+HOCOMOCOv11-full-C 

+                13 

 \end{Soutput}

 \end{Schunk}

 And 22 organisms (though the majority of the matrices come from just four):

@@ -109,7 +113,7 @@ And 22 organisms (though the majority of the matrices come from just four):

 \end{Sinput}

 \begin{Soutput}

                                                                      Hsapiens 

-                                                                         5016 

+                                                                         5384 

                                                                     Mmusculus 

                                                                          1411 

                                                                 Dmelanogaster 

@@ -257,14 +261,18 @@ all of the human matrices:

 > query (MotifDb, 'hsapiens')

 \end{Sinput}

 \begin{Soutput}

-MotifDb object of length 5031

+MotifDb object of length 5399

 | Created from downloaded public sources: 2013-Aug-30

-| 5031 position frequency matrices from 14 sources:

+| 5399 position frequency matrices from 18 sources:

 |         cisbp_1.02:  313

 |        HOCOMOCOv10:  640

-|       HOCOMOCOv11A:  181

-|       HOCOMOCOv11B:   84

-|       HOCOMOCOv11C:  135

+| HOCOMOCOv11-core-A:  181

+| HOCOMOCOv11-core-B:   84

+| HOCOMOCOv11-core-C:  135

+| HOCOMOCOv11-full-A:   46

+| HOCOMOCOv11-full-B:   19

+| HOCOMOCOv11-full-C:   13

+| HOCOMOCOv11-full-D:  290

 |               hPDI:  437

 |        JASPAR_2014:  117

 |        JASPAR_CORE:   66

@@ -275,7 +283,7 @@ MotifDb object of length 5031

 |       SwissRegulon:  684

 |           UniPROBE:    2

 | 8 organism/s

-|           Hsapiens: 5016

+|           Hsapiens: 5384

 | Mmusculus;Rnorvegicus;Hsapiens:    6

 | Mmusculus;Hsapiens:    3

 | Mmusculus;Rnorvegicus;Xlaevis;Stropicalis;Ggallus;Hsapiens;Btaurus;Ocuniculus:    2

@@ -301,14 +309,17 @@ If you want all matrices associated with \textbf{\emph{Sox}} transcription facto

 > query (MotifDb, 'sox')

 \end{Sinput}

 \begin{Soutput}

-MotifDb object of length 184

+MotifDb object of length 196

 | Created from downloaded public sources: 2013-Aug-30

-| 184 position frequency matrices from 14 sources:

+| 196 position frequency matrices from 17 sources:

 |    FlyFactorSurvey:    2

 |        HOCOMOCOv10:   25

-|       HOCOMOCOv11A:    1

-|       HOCOMOCOv11B:    5

-|       HOCOMOCOv11C:    2

+| HOCOMOCOv11-core-A:    1

+| HOCOMOCOv11-core-B:    5

+| HOCOMOCOv11-core-C:    2

+| HOCOMOCOv11-full-A:    2

+| HOCOMOCOv11-full-B:    1

+| HOCOMOCOv11-full-D:    9

 |              HOMER:    9

 |               hPDI:    2

 |        JASPAR_2014:    8

@@ -319,7 +330,7 @@ MotifDb object of length 184

 |       SwissRegulon:   19

 |           UniPROBE:   15

 | 7 organism/s

-|           Hsapiens:  103

+|           Hsapiens:  115

 |          Mmusculus:   67

 |      Dmelanogaster:    2

 | Mmusculus;Rnorvegicus;Hsapiens:    1

@@ -392,18 +403,22 @@ illustrate:

 \end{Sinput}

 \begin{Soutput}

  [1] "HOX-related factors{3.1.1}: CDX (Caudal type homeobox){3.1.1.9}"          

- [2] "TALE-type homeo domain factors{3.1.4}: MEIS{3.1.4.2}"                     

- [3] "Paired domain only{3.2.2}: PAX-2-like factors (partial homeobox){3.2.2.2}"

- [4] "Paired plus homeo domain{3.2.1}: PAX-4/6{3.2.1.2}"                        

- [5] "TALE-type homeo domain factors{3.1.4}: PBX{3.1.4.4}"                      

- [6] "TALE-type homeo domain factors{3.1.4}: PKNOX{3.1.4.5}"                    

- [7] "TALE-type homeo domain factors{3.1.4}: TGIF{3.1.4.6}"                     

- [8] "Homeo"                                                                    

- [9] "Homeo::Nuclear Factor I-CCAAT-binding"                                    

-[10] "Homeodomain"                                                              

-[11] "Paired plus homeo domain"                                                 

-[12] "TALE-type homeo domain factors"                                           

-[13] "homeodomain"                                                              

+ [2] "HOX-related factors{3.1.1}: GBX (Gastrulation brain homeobox){3.1.1.11}"  

+ [3] "TALE-type homeo domain factors{3.1.4}: IRX (Iroquois){3.1.4.1}"           

+ [4] "TALE-type homeo domain factors{3.1.4}: MEIS{3.1.4.2}"                     

+ [5] "Paired domain only{3.2.2}: PAX-1/9 (no homeo remnant){3.2.2.1}"           

+ [6] "Paired domain only{3.2.2}: PAX-2-like factors (partial homeobox){3.2.2.2}"

+ [7] "Paired plus homeo domain{3.2.1}: PAX-3/7{3.2.1.1}"                        

+ [8] "Paired plus homeo domain{3.2.1}: PAX-4/6{3.2.1.2}"                        

+ [9] "TALE-type homeo domain factors{3.1.4}: PBX{3.1.4.4}"                      

+[10] "TALE-type homeo domain factors{3.1.4}: PKNOX{3.1.4.5}"                    

+[11] "TALE-type homeo domain factors{3.1.4}: TGIF{3.1.4.6}"                     

+[12] "Homeo"                                                                    

+[13] "Homeo::Nuclear Factor I-CCAAT-binding"                                    

+[14] "Homeodomain"                                                              

+[15] "Paired plus homeo domain"                                                 

+[16] "TALE-type homeo domain factors"                                           

+[17] "homeodomain"                                                              

 \end{Soutput}

 \end{Schunk}

 \subsection{grep}

@@ -490,7 +505,7 @@ MotifDb object of length 17

 | Created from downloaded public sources: 2013-Aug-30

 | 17 position frequency matrices from 10 sources:

 |        HOCOMOCOv10:    3

-|       HOCOMOCOv11A:    1

+| HOCOMOCOv11-core-A:    1

 |              HOMER:    1

 |        JASPAR_2014:    1

 |        JASPAR_CORE:    1

@@ -805,7 +820,7 @@ pubmedID        26586801

                 Hsapiens-HOCOMOCOv11A-EGR1_HUMAN.H11MO.0.A                            

 providerName    EGR1_HUMAN.H11MO.0.A                                                  

 providerId      EGR1_HUMAN.H11MO.0.A                                                  

-dataSource      HOCOMOCOv11A                                                          

+dataSource      HOCOMOCOv11-core-A                                                    

 geneSymbol      EGR1                                                                  

 geneId          1958                                                                  

 geneIdType      ENTREZ                                                                

@@ -1033,7 +1048,7 @@ the grep solution, while serviceable, becomes a little awkward:

 > print (egr1.mouse.jaspar.rows)

 \end{Sinput}

 \begin{Soutput}

-[1] 3878 5032 6153

+[1] 4246 5400 6521

 \end{Soutput}

 \begin{Sinput}

 > egr1.motif <- MotifDb [egr1.mouse.jaspar.rows]