Browse code

non-core hocomocov11 motifs tagged 'full' now 'secondary'

paul-shannon authored on 18/03/2020 19:22:54
Showing5 changed files

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@@ -1,8 +1,8 @@
1 1
 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.29.3
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-Date: 2020-03-16
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+Version: 1.29.4
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+Date: 2020-03-18
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 Author: Paul Shannon, Matt Richards
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
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Binary files a/inst/extdata/hocomoco11.RData and b/inst/extdata/hocomoco11.RData differ
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@@ -1196,19 +1196,19 @@ test.hocomoco11.with.reliabilityScores <- function()
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    checkEquals(length(query(MotifDb, "hocomocov10")), 1066)
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    checkEquals(length(query(MotifDb, "hocomocov11")), 768)
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    checkEquals(length(query(MotifDb, "hocomocov11-core")), 400)
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-   checkEquals(length(query(MotifDb, "hocomocov11-full")), 368)
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+   checkEquals(length(query(MotifDb, "hocomocov11-secondary")), 368)
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    checkEquals(length(query(MotifDb, "hocomocov11-core-A")), 181)
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-   checkEquals(length(query(MotifDb, "hocomocov11-full-A")), 46)
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+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-A")), 46)
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    checkEquals(length(query(MotifDb, "hocomocov11-core-B")), 84)
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-   checkEquals(length(query(MotifDb, "hocomocov11-full-B")), 19)
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+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-B")), 19)
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    checkEquals(length(query(MotifDb, "hocomocov11-core-C")), 135)
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-   checkEquals(length(query(MotifDb, "hocomocov11-full-C")), 13)
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+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-C")), 13)
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    checkEquals(length(query(MotifDb, "hocomocov11-core-D")), 0)
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-   checkEquals(length(query(MotifDb, "hocomocov11-full-D")), 290)
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+   checkEquals(length(query(MotifDb, "hocomocov11-secondary-D")), 290)
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 } # test.hocomoco11.with.reliabilityScores
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 #------------------------------------------------------------------------------------------------------------------------
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Binary files a/vignettes/MotifDb-egr1.pdf and b/vignettes/MotifDb-egr1.pdf differ
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@@ -86,20 +86,24 @@ There are  more than two thousand  matrices, from five sources:
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 > length (MotifDb)
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 \end{Sinput}
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 \begin{Soutput}
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-[1] 10333
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+[1] 10701
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 \end{Soutput}
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 \begin{Sinput}
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 > sort (table (values (MotifDb)$dataSource), decreasing=TRUE)
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 \end{Sinput}
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 \begin{Soutput}
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-     jaspar2018      jaspar2016     HOCOMOCOv10      cisbp_1.02       jolma2013 
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-           1564            1209            1066             874             843 
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-   SwissRegulon         stamlab FlyFactorSurvey     JASPAR_2014     JASPAR_CORE 
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-            684             683             614             592             459 
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-           hPDI        UniPROBE           HOMER          ScerTF    HOCOMOCOv11A 
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-            437             380             332             196             181 
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-   HOCOMOCOv11C    HOCOMOCOv11B 
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-            135              84 
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+        jaspar2018         jaspar2016        HOCOMOCOv10         cisbp_1.02 
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+              1564               1209               1066                874 
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+         jolma2013       SwissRegulon            stamlab    FlyFactorSurvey 
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+               843                684                683                614 
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+       JASPAR_2014        JASPAR_CORE               hPDI           UniPROBE 
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+               592                459                437                380 
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+             HOMER HOCOMOCOv11-full-D             ScerTF HOCOMOCOv11-core-A 
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+               332                290                196                181 
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+HOCOMOCOv11-core-C HOCOMOCOv11-core-B HOCOMOCOv11-full-A HOCOMOCOv11-full-B 
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+               135                 84                 46                 19 
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+HOCOMOCOv11-full-C 
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+                13 
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 \end{Soutput}
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 \end{Schunk}
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 And 22 organisms (though the majority of the matrices come from just four):
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@@ -109,7 +113,7 @@ And 22 organisms (though the majority of the matrices come from just four):
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 \end{Sinput}
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 \begin{Soutput}
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                                                                      Hsapiens 
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-                                                                         5016 
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+                                                                         5384 
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                                                                     Mmusculus 
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                                                                          1411 
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                                                                 Dmelanogaster 
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@@ -257,14 +261,18 @@ all of the human matrices:
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 > query (MotifDb, 'hsapiens')
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 \end{Sinput}
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 \begin{Soutput}
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-MotifDb object of length 5031
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+MotifDb object of length 5399
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 | Created from downloaded public sources: 2013-Aug-30
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-| 5031 position frequency matrices from 14 sources:
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+| 5399 position frequency matrices from 18 sources:
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 |         cisbp_1.02:  313
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 |        HOCOMOCOv10:  640
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-|       HOCOMOCOv11A:  181
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-|       HOCOMOCOv11B:   84
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-|       HOCOMOCOv11C:  135
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+| HOCOMOCOv11-core-A:  181
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+| HOCOMOCOv11-core-B:   84
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+| HOCOMOCOv11-core-C:  135
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+| HOCOMOCOv11-full-A:   46
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+| HOCOMOCOv11-full-B:   19
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+| HOCOMOCOv11-full-C:   13
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+| HOCOMOCOv11-full-D:  290
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 |               hPDI:  437
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 |        JASPAR_2014:  117
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 |        JASPAR_CORE:   66
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@@ -275,7 +283,7 @@ MotifDb object of length 5031
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 |       SwissRegulon:  684
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 |           UniPROBE:    2
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 | 8 organism/s
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-|           Hsapiens: 5016
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+|           Hsapiens: 5384
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 | Mmusculus;Rnorvegicus;Hsapiens:    6
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 | Mmusculus;Hsapiens:    3
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 | Mmusculus;Rnorvegicus;Xlaevis;Stropicalis;Ggallus;Hsapiens;Btaurus;Ocuniculus:    2
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@@ -301,14 +309,17 @@ If you want all matrices associated with \textbf{\emph{Sox}} transcription facto
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 > query (MotifDb, 'sox')
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 \end{Sinput}
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 \begin{Soutput}
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-MotifDb object of length 184
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+MotifDb object of length 196
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 | Created from downloaded public sources: 2013-Aug-30
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-| 184 position frequency matrices from 14 sources:
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+| 196 position frequency matrices from 17 sources:
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 |    FlyFactorSurvey:    2
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 |        HOCOMOCOv10:   25
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-|       HOCOMOCOv11A:    1
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-|       HOCOMOCOv11B:    5
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-|       HOCOMOCOv11C:    2
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+| HOCOMOCOv11-core-A:    1
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+| HOCOMOCOv11-core-B:    5
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+| HOCOMOCOv11-core-C:    2
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+| HOCOMOCOv11-full-A:    2
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+| HOCOMOCOv11-full-B:    1
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+| HOCOMOCOv11-full-D:    9
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 |              HOMER:    9
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 |               hPDI:    2
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 |        JASPAR_2014:    8
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@@ -319,7 +330,7 @@ MotifDb object of length 184
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 |       SwissRegulon:   19
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 |           UniPROBE:   15
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 | 7 organism/s
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-|           Hsapiens:  103
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+|           Hsapiens:  115
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 |          Mmusculus:   67
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 |      Dmelanogaster:    2
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 | Mmusculus;Rnorvegicus;Hsapiens:    1
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@@ -392,18 +403,22 @@ illustrate:
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 \end{Sinput}
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 \begin{Soutput}
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  [1] "HOX-related factors{3.1.1}: CDX (Caudal type homeobox){3.1.1.9}"          
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- [2] "TALE-type homeo domain factors{3.1.4}: MEIS{3.1.4.2}"                     
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- [3] "Paired domain only{3.2.2}: PAX-2-like factors (partial homeobox){3.2.2.2}"
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- [4] "Paired plus homeo domain{3.2.1}: PAX-4/6{3.2.1.2}"                        
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- [5] "TALE-type homeo domain factors{3.1.4}: PBX{3.1.4.4}"                      
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- [6] "TALE-type homeo domain factors{3.1.4}: PKNOX{3.1.4.5}"                    
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- [7] "TALE-type homeo domain factors{3.1.4}: TGIF{3.1.4.6}"                     
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- [8] "Homeo"                                                                    
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- [9] "Homeo::Nuclear Factor I-CCAAT-binding"                                    
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-[10] "Homeodomain"                                                              
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-[11] "Paired plus homeo domain"                                                 
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-[12] "TALE-type homeo domain factors"                                           
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-[13] "homeodomain"                                                              
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+ [2] "HOX-related factors{3.1.1}: GBX (Gastrulation brain homeobox){3.1.1.11}"  
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+ [3] "TALE-type homeo domain factors{3.1.4}: IRX (Iroquois){3.1.4.1}"           
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+ [4] "TALE-type homeo domain factors{3.1.4}: MEIS{3.1.4.2}"                     
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+ [5] "Paired domain only{3.2.2}: PAX-1/9 (no homeo remnant){3.2.2.1}"           
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+ [6] "Paired domain only{3.2.2}: PAX-2-like factors (partial homeobox){3.2.2.2}"
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+ [7] "Paired plus homeo domain{3.2.1}: PAX-3/7{3.2.1.1}"                        
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+ [8] "Paired plus homeo domain{3.2.1}: PAX-4/6{3.2.1.2}"                        
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+ [9] "TALE-type homeo domain factors{3.1.4}: PBX{3.1.4.4}"                      
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+[10] "TALE-type homeo domain factors{3.1.4}: PKNOX{3.1.4.5}"                    
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+[11] "TALE-type homeo domain factors{3.1.4}: TGIF{3.1.4.6}"                     
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+[12] "Homeo"                                                                    
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+[13] "Homeo::Nuclear Factor I-CCAAT-binding"                                    
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+[14] "Homeodomain"                                                              
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+[15] "Paired plus homeo domain"                                                 
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+[16] "TALE-type homeo domain factors"                                           
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+[17] "homeodomain"                                                              
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 \end{Soutput}
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 \end{Schunk}
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 \subsection{grep}
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@@ -490,7 +505,7 @@ MotifDb object of length 17
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 | Created from downloaded public sources: 2013-Aug-30
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 | 17 position frequency matrices from 10 sources:
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 |        HOCOMOCOv10:    3
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-|       HOCOMOCOv11A:    1
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+| HOCOMOCOv11-core-A:    1
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 |              HOMER:    1
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 |        JASPAR_2014:    1
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 |        JASPAR_CORE:    1
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@@ -805,7 +820,7 @@ pubmedID        26586801
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                 Hsapiens-HOCOMOCOv11A-EGR1_HUMAN.H11MO.0.A                            
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 providerName    EGR1_HUMAN.H11MO.0.A                                                  
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 providerId      EGR1_HUMAN.H11MO.0.A                                                  
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-dataSource      HOCOMOCOv11A                                                          
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+dataSource      HOCOMOCOv11-core-A                                                    
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 geneSymbol      EGR1                                                                  
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 geneId          1958                                                                  
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 geneIdType      ENTREZ                                                                
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@@ -1033,7 +1048,7 @@ the grep solution, while serviceable, becomes a little awkward:
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 > print (egr1.mouse.jaspar.rows)
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 \end{Sinput}
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 \begin{Soutput}
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-[1] 3878 5032 6153
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+[1] 4246 5400 6521
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 \end{Soutput}
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 \begin{Sinput}
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 > egr1.motif <- MotifDb [egr1.mouse.jaspar.rows]