| ... | ... |
@@ -1,14 +1,14 @@ |
| 1 | 1 |
Package: MotifDb |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs |
| 4 |
-Version: 1.19.19 |
|
| 5 |
-Date: 2017-12-07 |
|
| 4 |
+Version: 1.19.20 |
|
| 5 |
+Date: 2018-01-23 |
|
| 6 | 6 |
Author: Paul Shannon, Matt Richards |
| 7 | 7 |
Maintainer: Paul Shannon <pshannon@systemsbiology.org> |
| 8 | 8 |
Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings |
| 9 | 9 |
Suggests: RUnit, seqLogo, MotIV |
| 10 | 10 |
Imports: rtracklayer, splitstackshape |
| 11 |
-Description: More than 8000 annotated position frequency matrices from 13 public sources, for multiple organisms. |
|
| 11 |
+Description: More than 9000 annotated position frequency matrices from 14 public sources, for multiple organisms. |
|
| 12 | 12 |
License: Artistic-2.0 | file LICENSE |
| 13 | 13 |
License_is_FOSS: no |
| 14 | 14 |
License_restricts_use: yes |
| ... | ... |
@@ -777,6 +777,40 @@ test.geneToMotif <- function() |
| 777 | 777 |
# MotifDb for ATF5 |
| 778 | 778 |
# todo: compare the MA0110596_1.02 matrix of cisp_1.02 to japar MA0833.1 |
| 779 | 779 |
|
| 780 |
+} # test.geneToMotif |
|
| 781 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 782 |
+# sad to say I do not recall what problem/fix is tested here (pshannon, 23 jan 2018). |
|
| 783 |
+# however, it demonstrates the variety of results which can be returned by non-jaspar datasets |
|
| 784 |
+# when using the MotifDb mapping source, and the relative paucity which is sometimes |
|
| 785 |
+# seen with the TFclass mapper |
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| 786 |
+test.geneToMotif.ignore.jasparSuffixes <- function() |
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| 787 |
+{
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| 788 |
+ printf("--- test.geneToMotif.ignore.jasparSuffixes")
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|
| 789 |
+ mdb <- MotifDb |
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| 790 |
+ |
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| 791 |
+ genes <- c("FOS", "ATF5", "bogus")
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|
| 792 |
+ |
|
| 793 |
+ # use TFClass family classifcation |
|
| 794 |
+ tbl.tfClass <- geneToMotif(mdb, genes, source="TfClaSS") # intentional mis-capitalization |
|
| 795 |
+ checkEquals(sort(tbl.tfClass$gene), sort(c("ATF5", "FOS", "FOS")))
|
|
| 796 |
+ checkEquals(sort(tbl.tfClass$motif), sort(c("MA0833.1", "MA0099.2", "MA0476.1")))
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|
| 797 |
+ checkEquals(tbl.tfClass$source, rep("TFClass", 3))
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|
| 798 |
+ |
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| 799 |
+ # MotifDb mode uses the MotifDb metadata, pulled from many sources |
|
| 800 |
+ tbl.mdb <- geneToMotif(mdb, genes, source="mOtifdb") # intentional mis-capitalization |
|
| 801 |
+ checkEquals(dim(tbl.mdb), c(13, 6)) |
|
| 802 |
+ checkEquals(subset(tbl.mdb, dataSource=="jaspar2016" & geneSymbol== "FOS")$motif, "MA0476.1") |
|
| 803 |
+ # no recognizable (i.e., jaspar standard) motif name returned by MotifDb metadata |
|
| 804 |
+ # MotifDb for ATF5 |
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| 805 |
+ |
|
| 806 |
+ # compare the MA0110599_1.02 matrix of cisp_1.02 to japar MA0476.1: the identical matrix! |
|
| 807 |
+ # 1 FOS MA0110599_1.02 cisbp_1.02 Hsapiens 24194598 MotifDb |
|
| 808 |
+ # 10 FOS MA0476.1 jaspar2018 Hsapiens 17916232 MotifDb |
|
| 809 |
+ # this establishes the need for careful scrutiny as one winnows a geneToMotif result into |
|
| 810 |
+ # useful non-reduplicative sequence analysis |
|
| 811 |
+ |
|
| 812 |
+ checkEquals(as.list(query(mdb, "MA0110599")), as.list(query(query(mdb, "MA0476.1"), "jaspar2018"))) |
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| 813 |
+ |
|
| 780 | 814 |
} # test.geneToMotif |
| 781 | 815 |
#------------------------------------------------------------------------------------------------------------------------ |
| 782 | 816 |
test.motifToGene <- function() |
