git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@86069 bc3139a8-67e5-0310-9ffc-ced21a209358
p.shannon authored on 04/02/2014 19:33:01
| ... | ... |
@@ -102,7 +102,7 @@ test.createMetadataTable = function (x.matrices, x.novels) |
| 102 | 102 |
"bindingDomain", "tfFamily", "experimentType", "pubmedID")) |
| 103 | 103 |
checkEquals (tbl.md$providerName [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
|
| 104 | 104 |
checkEquals (tbl.md$providerId [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
|
| 105 |
- checkEquals (tbl.md$pubmedID [1:2], c ('22959076', '22959076'))
|
|
| 105 |
+ checkEquals (tbl.md$pubmedID [1:2], c ("22955618", "22955618"))
|
|
| 106 | 106 |
checkEquals (tbl.md$dataSource [1:2], c ('stamlab', 'stamlab'))
|
| 107 | 107 |
checkEquals (tbl.md$organism [1:2], c ('Hsapiens', 'Hsapiens'))
|
| 108 | 108 |
checkEquals (tbl.md$experimentType [1:2], c ('digital genomic footprinting', 'digital genomic footprinting'))
|
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@86014 bc3139a8-67e5-0310-9ffc-ced21a209358
p.shannon authored on 03/02/2014 19:40:10
| ... | ... |
@@ -93,13 +93,13 @@ test.createAnnotationTable = function () |
| 93 | 93 |
#------------------------------------------------------------------------------------------------------------------------ |
| 94 | 94 |
test.createMetadataTable = function (x.matrices, x.novels) |
| 95 | 95 |
{
|
| 96 |
- print ('--- test.createMetadataTable')
|
|
| 97 |
- # try it first with just two matrices |
|
| 98 |
- tbl.md = createMetadataTable (x.matrices [1:12], x.novels [1:12]) |
|
| 99 |
- checkEquals (dim (tbl.md), c (12, 15)) |
|
| 100 |
- checkEquals (colnames (tbl.md), c ("providerName", "providerId", "dataSource", "geneSymbol", "geneId", "geneIdType",
|
|
| 101 |
- "proteinId", "proteinIdType", "organism", "sequenceCount", "bindingSequence", |
|
| 102 |
- "bindingDomain", "tfFamily", "experimentType", "pubmedID")) |
|
| 96 |
+ print ('--- test.createMetadataTable')
|
|
| 97 |
+ # try it first with just two matrices |
|
| 98 |
+ tbl.md = createMetadataTable (x.matrices [1:12], x.novels [1:12]) |
|
| 99 |
+ checkEquals (dim (tbl.md), c (12, 15)) |
|
| 100 |
+ checkEquals (colnames (tbl.md), c ("providerName", "providerId", "dataSource", "geneSymbol", "geneId", "geneIdType",
|
|
| 101 |
+ "proteinId", "proteinIdType", "organism", "sequenceCount", "bindingSequence", |
|
| 102 |
+ "bindingDomain", "tfFamily", "experimentType", "pubmedID")) |
|
| 103 | 103 |
checkEquals (tbl.md$providerName [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
|
| 104 | 104 |
checkEquals (tbl.md$providerId [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
|
| 105 | 105 |
checkEquals (tbl.md$pubmedID [1:2], c ('22959076', '22959076'))
|
| ... | ... |
@@ -107,8 +107,9 @@ test.createMetadataTable = function (x.matrices, x.novels) |
| 107 | 107 |
checkEquals (tbl.md$organism [1:2], c ('Hsapiens', 'Hsapiens'))
|
| 108 | 108 |
checkEquals (tbl.md$experimentType [1:2], c ('digital genomic footprinting', 'digital genomic footprinting'))
|
| 109 | 109 |
checkEquals (tbl.md$geneId, c (rep ('knownMotif', 11), 'novelMotif'))
|
| 110 |
+ checkTrue(all(is.na(tbl.md$geneIdType))) |
|
| 110 | 111 |
|
| 111 |
- invisible (tbl.md) |
|
| 112 |
+ invisible (tbl.md) |
|
| 112 | 113 |
|
| 113 | 114 |
} # test.createMetadataTable |
| 114 | 115 |
#------------------------------------------------------------------------------------------------------------------------ |
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75382 bc3139a8-67e5-0310-9ffc-ced21a209358
p.shannon authored on 05/04/2013 20:36:31
| ... | ... |
@@ -6,7 +6,7 @@ library (RUnit) |
| 6 | 6 |
#------------------------------------------------------------------------------------------------------------------------ |
| 7 | 7 |
source("import.R")
|
| 8 | 8 |
#------------------------------------------------------------------------------------------------------------------------ |
| 9 |
-run.tests = function (dataDir=kDataDir) |
|
| 9 |
+run.tests = function (dataDir) |
|
| 10 | 10 |
{
|
| 11 | 11 |
dataDir <- file.path(dataDir, "stamlab") |
| 12 | 12 |
x.rawMatrixList <<- test.readRawMatrices (dataDir) |
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75368 bc3139a8-67e5-0310-9ffc-ced21a209358
p.shannon authored on 05/04/2013 17:35:26
| ... | ... |
@@ -8,6 +8,7 @@ source("import.R")
|
| 8 | 8 |
#------------------------------------------------------------------------------------------------------------------------ |
| 9 | 9 |
run.tests = function (dataDir=kDataDir) |
| 10 | 10 |
{
|
| 11 |
+ dataDir <- file.path(dataDir, "stamlab") |
|
| 11 | 12 |
x.rawMatrixList <<- test.readRawMatrices (dataDir) |
| 12 | 13 |
x.novels <<- test.readNovelStatus (dataDir) |
| 13 | 14 |
x.matrices <<- test.extractAndNormalizeMatrices (x.rawMatrixList) |
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75345 bc3139a8-67e5-0310-9ffc-ced21a209358
p.shannon authored on 05/04/2013 13:35:38
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,210 @@ |
| 1 |
+# stamlab/test.R |
|
| 2 |
+# notes: 3 matrices come w/o speciesID, tax = 'vertebrates'. not our problem to fix, at least not yet. |
|
| 3 |
+# TBP, HNF4A and CEBPA (MA0108.2, MA0114.1, MA0102.2) |
|
| 4 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 5 |
+library (RUnit) |
|
| 6 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 7 |
+source("import.R")
|
|
| 8 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 9 |
+run.tests = function (dataDir=kDataDir) |
|
| 10 |
+{
|
|
| 11 |
+ x.rawMatrixList <<- test.readRawMatrices (dataDir) |
|
| 12 |
+ x.novels <<- test.readNovelStatus (dataDir) |
|
| 13 |
+ x.matrices <<- test.extractAndNormalizeMatrices (x.rawMatrixList) |
|
| 14 |
+ x.tbl.md <<- test.createMetadataTable (x.matrices, x.novels) |
|
| 15 |
+ x.matrices.renamed <<- test.renameMatrices (x.matrices, x.tbl.md) |
|
| 16 |
+ |
|
| 17 |
+} # run.tests |
|
| 18 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 19 |
+test.readRawMatrices = function (dataDir) |
|
| 20 |
+{
|
|
| 21 |
+ print ('--- test.readMatrices')
|
|
| 22 |
+ list.pwms = readRawMatrices (dataDir) |
|
| 23 |
+ checkEquals (length (list.pwms), 683) |
|
| 24 |
+ checkEquals (names (list.pwms [[1]]), c ("title", "consensus.sequence", "matrix"))
|
|
| 25 |
+ checkEquals (rownames (list.pwms[[1]]$matrix), c ("A", "C", "G", "T"))
|
|
| 26 |
+ invisible (list.pwms) |
|
| 27 |
+ |
|
| 28 |
+} # test.readRawMatrices |
|
| 29 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 30 |
+test.readNovelStatus = function (dataDir) |
|
| 31 |
+{
|
|
| 32 |
+ print ('--- test.readNovelStatus')
|
|
| 33 |
+ novel.status = readNovelStatus (dataDir) |
|
| 34 |
+ checkEquals (length (novel.status), 683) |
|
| 35 |
+ checkEquals (length (which (novel.status == TRUE)), 289) |
|
| 36 |
+ # do a spot check around first novel in novels.txt |
|
| 37 |
+ checkEquals (as.logical (novel.status [c ('UW.Motif.0010', 'UW.Motif.0011', 'UW.Motif.0012')]),
|
|
| 38 |
+ c (FALSE, FALSE, TRUE)) |
|
| 39 |
+ invisible (novel.status) |
|
| 40 |
+ |
|
| 41 |
+} # readNovelStatus |
|
| 42 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 43 |
+test.extractAndNormalizeMatrices = function (x.rawMatrixList) |
|
| 44 |
+{
|
|
| 45 |
+ print ('--- test.extractAndNormalizeMatrices')
|
|
| 46 |
+ matrices.fixed <<- extractAndNormalizeMatrices (x.rawMatrixList) |
|
| 47 |
+ # make sure a UW.Motif.0nnn name accompanies each matrix |
|
| 48 |
+ checkEquals (length (grep ('UW.Motif.0', names (matrices.fixed))), length (matrices.fixed))
|
|
| 49 |
+ # make sure all columns in all matrices sum to 1.0 |
|
| 50 |
+ checkTrue (all (sapply (matrices.fixed, function (m) all (abs (colSums (m) - 1.0) < 1e-10)))) |
|
| 51 |
+ invisible (matrices.fixed) |
|
| 52 |
+ |
|
| 53 |
+} # test.extractAndNormalizeMatrices |
|
| 54 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 55 |
+test.convertRawMatricesToStandard = function (tbl.rmat) |
|
| 56 |
+{
|
|
| 57 |
+ print ('--- test.convertRawMatricesToStandard')
|
|
| 58 |
+ # get just the first two raw matrices |
|
| 59 |
+ |
|
| 60 |
+ first.two.ids = head (unique (tbl.rmat$id), n=2) |
|
| 61 |
+ rows = nrow (subset (tbl.rmat, id %in% first.two.ids)) |
|
| 62 |
+ matrices = convertRawMatricesToStandard (tbl.rmat [1:rows,]) |
|
| 63 |
+ checkEquals (length (matrices), 2) |
|
| 64 |
+ checkEquals (names (matrices), first.two.ids) |
|
| 65 |
+ |
|
| 66 |
+ # it will not always be true, but IS true for the first two matrices, currently "9229" and "9231", that there |
|
| 67 |
+ # are an equal number of nucleotides at each position. |
|
| 68 |
+ checkTrue (all (colSums (matrices [[1]]) == 97)) |
|
| 69 |
+ checkTrue (all (colSums (matrices [[2]]) == 185)) |
|
| 70 |
+ |
|
| 71 |
+ # now run all the matrices through |
|
| 72 |
+ matrices = convertRawMatricesToStandard (tbl.rmat) |
|
| 73 |
+ checkEquals (length (matrices), 459) |
|
| 74 |
+ checkEquals (names (matrices)[1:2], first.two.ids) |
|
| 75 |
+ |
|
| 76 |
+ invisible (matrices) |
|
| 77 |
+ |
|
| 78 |
+} # test.convertRawMatricesToStandard |
|
| 79 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 80 |
+test.createAnnotationTable = function () |
|
| 81 |
+{
|
|
| 82 |
+ print ('--- test.createAnnotationTable')
|
|
| 83 |
+ tbl.anno = createAnnotationTable () |
|
| 84 |
+ checkEquals (dim (tbl.anno), c (513, 13)) |
|
| 85 |
+ expected = c ("fullID", "id", "category", "mID", "version", "binder", "speciesID", "proteinID", "family", "tax", "class", "pubmed", "type")
|
|
| 86 |
+ checkEquals (colnames (tbl.anno), expected) |
|
| 87 |
+ |
|
| 88 |
+ checkEquals (head (tbl.anno$fullID), c ("MA0001.1", "MA0003.1", "MA0004.1", "MA0005.1", "MA0006.1", "MA0006.1"))
|
|
| 89 |
+ invisible (tbl.anno) |
|
| 90 |
+ |
|
| 91 |
+} # test.createAnnotationTable |
|
| 92 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 93 |
+test.createMetadataTable = function (x.matrices, x.novels) |
|
| 94 |
+{
|
|
| 95 |
+ print ('--- test.createMetadataTable')
|
|
| 96 |
+ # try it first with just two matrices |
|
| 97 |
+ tbl.md = createMetadataTable (x.matrices [1:12], x.novels [1:12]) |
|
| 98 |
+ checkEquals (dim (tbl.md), c (12, 15)) |
|
| 99 |
+ checkEquals (colnames (tbl.md), c ("providerName", "providerId", "dataSource", "geneSymbol", "geneId", "geneIdType",
|
|
| 100 |
+ "proteinId", "proteinIdType", "organism", "sequenceCount", "bindingSequence", |
|
| 101 |
+ "bindingDomain", "tfFamily", "experimentType", "pubmedID")) |
|
| 102 |
+ checkEquals (tbl.md$providerName [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
|
|
| 103 |
+ checkEquals (tbl.md$providerId [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
|
|
| 104 |
+ checkEquals (tbl.md$pubmedID [1:2], c ('22959076', '22959076'))
|
|
| 105 |
+ checkEquals (tbl.md$dataSource [1:2], c ('stamlab', 'stamlab'))
|
|
| 106 |
+ checkEquals (tbl.md$organism [1:2], c ('Hsapiens', 'Hsapiens'))
|
|
| 107 |
+ checkEquals (tbl.md$experimentType [1:2], c ('digital genomic footprinting', 'digital genomic footprinting'))
|
|
| 108 |
+ checkEquals (tbl.md$geneId, c (rep ('knownMotif', 11), 'novelMotif'))
|
|
| 109 |
+ |
|
| 110 |
+ invisible (tbl.md) |
|
| 111 |
+ |
|
| 112 |
+} # test.createMetadataTable |
|
| 113 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 114 |
+test.renameMatrices = function (matrices, tbl.md) |
|
| 115 |
+{
|
|
| 116 |
+ print("--- test.renameMatrices")
|
|
| 117 |
+ |
|
| 118 |
+ # try it with just the first two matrices |
|
| 119 |
+ matrix.pair = matrices [1:2] |
|
| 120 |
+ tbl.pair = tbl.md [1:2,] |
|
| 121 |
+ matrix.pair.renamed = renameMatrices (matrix.pair, tbl.pair) |
|
| 122 |
+ checkEquals (names (matrix.pair.renamed), c ("Hsapiens-stamlab-UW.Motif.0001", "Hsapiens-stamlab-UW.Motif.0002"))
|
|
| 123 |
+ |
|
| 124 |
+} # test.renameMatrices |
|
| 125 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 126 |
+test.convertTaxonCode = function () |
|
| 127 |
+{
|
|
| 128 |
+ print ('--- test.convertTaxonCode')
|
|
| 129 |
+ |
|
| 130 |
+ checkEquals (convertTaxonCode ('9606'), 'Hsapiens')
|
|
| 131 |
+ checkEquals (convertTaxonCode (9606), 'Hsapiens') |
|
| 132 |
+ # anomalous codes, which an examination of the jaspar website reveals as 'vertebrates' |
|
| 133 |
+ checkEquals (convertTaxonCode (NA), 'Vertebrata') |
|
| 134 |
+ checkEquals (convertTaxonCode ('NA'), 'Vertebrata')
|
|
| 135 |
+ checkEquals (convertTaxonCode (NA_character_), 'Vertebrata') |
|
| 136 |
+ checkEquals (convertTaxonCode ('-'), 'Vertebrata')
|
|
| 137 |
+ |
|
| 138 |
+} # test.convertTaxonCode |
|
| 139 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 140 |
+test.guessProteinIdentifierType = function (moleculeName) |
|
| 141 |
+{
|
|
| 142 |
+ print ('--- test.guessProteinIdentifierType')
|
|
| 143 |
+ checkEquals (guessProteinIdentifierType ('P29383'), 'UNIPROT')
|
|
| 144 |
+ |
|
| 145 |
+ all.types = sapply (x.tbl.anno$proteinID, guessProteinIdentifierType) |
|
| 146 |
+ checkTrue (length (which (is.na (all.types))) < 12) # got most of them. |
|
| 147 |
+ |
|
| 148 |
+} # test.guessProteinIdentifierType |
|
| 149 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 150 |
+test.normalizeMatrices = function (matrices) |
|
| 151 |
+{
|
|
| 152 |
+ print ('--- test.normalizeMatrices')
|
|
| 153 |
+ |
|
| 154 |
+ colsums = as.integer (sapply (matrices, function (mtx) as.integer (mean (round (colSums (mtx)))))) |
|
| 155 |
+ #checkTrue (all (colsums > 1)) |
|
| 156 |
+ |
|
| 157 |
+ matrices.norm = normalizeMatrices (matrices) |
|
| 158 |
+ |
|
| 159 |
+ colsums = as.integer (sapply (matrices.norm, function (mtx) as.integer (mean (round (colSums (mtx)))))) |
|
| 160 |
+ checkTrue (all (colsums == 1)) |
|
| 161 |
+ |
|
| 162 |
+ invisible (matrices.norm) |
|
| 163 |
+ |
|
| 164 |
+} # test.normalizeMatrices |
|
| 165 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 166 |
+test.assignGeneId = function (proteinId) |
|
| 167 |
+{
|
|
| 168 |
+ print ('--- test.assignGeneId')
|
|
| 169 |
+ uniprot.ids = c ('Q9GRA5', 'P31314', 'AAC18941', 'O49397')
|
|
| 170 |
+ refseq.ids = c ('NP_995315.1', 'NP_032840', 'NP_599022')
|
|
| 171 |
+ yeast.ids = c ('YKL112W', 'YMR072W', 'YLR131C')
|
|
| 172 |
+ |
|
| 173 |
+ checkEquals (assignGeneId ('NP_995315.1'), list (geneId='4782', type='ENTREZ'))
|
|
| 174 |
+ checkEquals (assignGeneId ('NP_599022'), list (geneId='6095', type='ENTREZ'))
|
|
| 175 |
+ |
|
| 176 |
+ checkEquals (assignGeneId ('P31314'), list (geneId='3195', type='ENTREZ'))
|
|
| 177 |
+ |
|
| 178 |
+ checkEquals (assignGeneId ('YKL112W'), list (geneId='YKL112W', type='SGD'))
|
|
| 179 |
+ |
|
| 180 |
+ # see how successful this is over all 513 proteinIds |
|
| 181 |
+ |
|
| 182 |
+ tbl.anno = createAnnotationTable () |
|
| 183 |
+ mtx.geneId = as.data.frame (t (sapply (tbl.anno$proteinID, assignGeneId))) |
|
| 184 |
+ tbl.types = as.data.frame (table (as.character (mtx.geneId$type), useNA='always'), stringsAsFactors=FALSE) |
|
| 185 |
+ checkEquals (tbl.types$Var1, c ("ENTREZ", "SGD", NA))
|
|
| 186 |
+ checkEquals (tbl.types$Freq, c (141, 177, 195)) |
|
| 187 |
+ |
|
| 188 |
+} # test.assignGeneId |
|
| 189 |
+#------------------------------------------------------------------------------------------------------------------------ |
|
| 190 |
+test.parsePwm = function () |
|
| 191 |
+{
|
|
| 192 |
+ print ('--- test.parsePwm')
|
|
| 193 |
+ lines = c ('UW.Motif.0006 aggaaatg',
|
|
| 194 |
+ '0.890585 0.007855 0.051323 0.050237', |
|
| 195 |
+ '0.060732 0.004506 0.894170 0.040593', |
|
| 196 |
+ '0.072765 0.037935 0.860704 0.028596', |
|
| 197 |
+ '0.929585 0.024037 0.034914 0.011464', |
|
| 198 |
+ '0.931220 0.023231 0.029078 0.016471', |
|
| 199 |
+ '0.857934 0.044211 0.072594 0.025261', |
|
| 200 |
+ '0.065840 0.013777 0.058013 0.862370', |
|
| 201 |
+ '0.049937 0.036238 0.861871 0.051953') |
|
| 202 |
+ m6 = parsePwm (lines) |
|
| 203 |
+ checkEquals (names (m6), c ("title", "consensus.sequence", "matrix"))
|
|
| 204 |
+ pwm = m6$matrix |
|
| 205 |
+ checkEquals (dim (pwm), c (4, 8)) |
|
| 206 |
+ checkEquals (rownames (pwm), c ('A', 'C', 'G', 'T'))
|
|
| 207 |
+ invisible (m6) |
|
| 208 |
+ |
|
| 209 |
+} # test.parsePwm |
|
| 210 |
+#------------------------------------------------------------------------------------------------------------------------ |