# stamlab/test.R
# notes: 3 matrices come w/o speciesID, tax = 'vertebrates'. not our problem to fix, at least not yet.
# TBP, HNF4A and CEBPA (MA0108.2, MA0114.1, MA0102.2)
#------------------------------------------------------------------------------------------------------------------------
library (RUnit)
#------------------------------------------------------------------------------------------------------------------------
source("import.R")
#------------------------------------------------------------------------------------------------------------------------
run.tests = function (dataDir)
{
dataDir <- file.path(dataDir, "stamlab")
x.rawMatrixList <<- test.readRawMatrices (dataDir)
x.novels <<- test.readNovelStatus (dataDir)
x.matrices <<- test.extractAndNormalizeMatrices (x.rawMatrixList)
x.tbl.md <<- test.createMetadataTable (x.matrices, x.novels)
x.matrices.renamed <<- test.renameMatrices (x.matrices, x.tbl.md)
} # run.tests
#------------------------------------------------------------------------------------------------------------------------
test.readRawMatrices = function (dataDir)
{
print ('--- test.readMatrices')
list.pwms = readRawMatrices (dataDir)
checkEquals (length (list.pwms), 683)
checkEquals (names (list.pwms [[1]]), c ("title", "consensus.sequence", "matrix"))
checkEquals (rownames (list.pwms[[1]]$matrix), c ("A", "C", "G", "T"))
invisible (list.pwms)
} # test.readRawMatrices
#------------------------------------------------------------------------------------------------------------------------
test.readNovelStatus = function (dataDir)
{
print ('--- test.readNovelStatus')
novel.status = readNovelStatus (dataDir)
checkEquals (length (novel.status), 683)
checkEquals (length (which (novel.status == TRUE)), 289)
# do a spot check around first novel in novels.txt
checkEquals (as.logical (novel.status [c ('UW.Motif.0010', 'UW.Motif.0011', 'UW.Motif.0012')]),
c (FALSE, FALSE, TRUE))
invisible (novel.status)
} # readNovelStatus
#------------------------------------------------------------------------------------------------------------------------
test.extractAndNormalizeMatrices = function (x.rawMatrixList)
{
print ('--- test.extractAndNormalizeMatrices')
matrices.fixed <<- extractAndNormalizeMatrices (x.rawMatrixList)
# make sure a UW.Motif.0nnn name accompanies each matrix
checkEquals (length (grep ('UW.Motif.0', names (matrices.fixed))), length (matrices.fixed))
# make sure all columns in all matrices sum to 1.0
checkTrue (all (sapply (matrices.fixed, function (m) all (abs (colSums (m) - 1.0) < 1e-10))))
invisible (matrices.fixed)
} # test.extractAndNormalizeMatrices
#------------------------------------------------------------------------------------------------------------------------
test.convertRawMatricesToStandard = function (tbl.rmat)
{
print ('--- test.convertRawMatricesToStandard')
# get just the first two raw matrices
first.two.ids = head (unique (tbl.rmat$id), n=2)
rows = nrow (subset (tbl.rmat, id %in% first.two.ids))
matrices = convertRawMatricesToStandard (tbl.rmat [1:rows,])
checkEquals (length (matrices), 2)
checkEquals (names (matrices), first.two.ids)
# it will not always be true, but IS true for the first two matrices, currently "9229" and "9231", that there
# are an equal number of nucleotides at each position.
checkTrue (all (colSums (matrices [[1]]) == 97))
checkTrue (all (colSums (matrices [[2]]) == 185))
# now run all the matrices through
matrices = convertRawMatricesToStandard (tbl.rmat)
checkEquals (length (matrices), 459)
checkEquals (names (matrices)[1:2], first.two.ids)
invisible (matrices)
} # test.convertRawMatricesToStandard
#------------------------------------------------------------------------------------------------------------------------
test.createAnnotationTable = function ()
{
print ('--- test.createAnnotationTable')
tbl.anno = createAnnotationTable ()
checkEquals (dim (tbl.anno), c (513, 13))
expected = c ("fullID", "id", "category", "mID", "version", "binder", "speciesID", "proteinID", "family", "tax", "class", "pubmed", "type")
checkEquals (colnames (tbl.anno), expected)
checkEquals (head (tbl.anno$fullID), c ("MA0001.1", "MA0003.1", "MA0004.1", "MA0005.1", "MA0006.1", "MA0006.1"))
invisible (tbl.anno)
} # test.createAnnotationTable
#------------------------------------------------------------------------------------------------------------------------
test.createMetadataTable = function (x.matrices, x.novels)
{
print ('--- test.createMetadataTable')
# try it first with just two matrices
tbl.md = createMetadataTable (x.matrices [1:12], x.novels [1:12])
checkEquals (dim (tbl.md), c (12, 15))
checkEquals (colnames (tbl.md), c ("providerName", "providerId", "dataSource", "geneSymbol", "geneId", "geneIdType",
"proteinId", "proteinIdType", "organism", "sequenceCount", "bindingSequence",
"bindingDomain", "tfFamily", "experimentType", "pubmedID"))
checkEquals (tbl.md$providerName [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
checkEquals (tbl.md$providerId [1:2], c ('UW.Motif.0001', 'UW.Motif.0002'))
checkEquals (tbl.md$pubmedID [1:2], c ("22955618", "22955618"))
checkEquals (tbl.md$dataSource [1:2], c ('stamlab', 'stamlab'))
checkEquals (tbl.md$organism [1:2], c ('Hsapiens', 'Hsapiens'))
checkEquals (tbl.md$experimentType [1:2], c ('digital genomic footprinting', 'digital genomic footprinting'))
checkEquals (tbl.md$geneId, c (rep ('knownMotif', 11), 'novelMotif'))
checkTrue(all(is.na(tbl.md$geneIdType)))
invisible (tbl.md)
} # test.createMetadataTable
#------------------------------------------------------------------------------------------------------------------------
test.renameMatrices = function (matrices, tbl.md)
{
print("--- test.renameMatrices")
# try it with just the first two matrices
matrix.pair = matrices [1:2]
tbl.pair = tbl.md [1:2,]
matrix.pair.renamed = renameMatrices (matrix.pair, tbl.pair)
checkEquals (names (matrix.pair.renamed), c ("Hsapiens-stamlab-UW.Motif.0001", "Hsapiens-stamlab-UW.Motif.0002"))
} # test.renameMatrices
#------------------------------------------------------------------------------------------------------------------------
test.convertTaxonCode = function ()
{
print ('--- test.convertTaxonCode')
checkEquals (convertTaxonCode ('9606'), 'Hsapiens')
checkEquals (convertTaxonCode (9606), 'Hsapiens')
# anomalous codes, which an examination of the jaspar website reveals as 'vertebrates'
checkEquals (convertTaxonCode (NA), 'Vertebrata')
checkEquals (convertTaxonCode ('NA'), 'Vertebrata')
checkEquals (convertTaxonCode (NA_character_), 'Vertebrata')
checkEquals (convertTaxonCode ('-'), 'Vertebrata')
} # test.convertTaxonCode
#------------------------------------------------------------------------------------------------------------------------
test.guessProteinIdentifierType = function (moleculeName)
{
print ('--- test.guessProteinIdentifierType')
checkEquals (guessProteinIdentifierType ('P29383'), 'UNIPROT')
all.types = sapply (x.tbl.anno$proteinID, guessProteinIdentifierType)
checkTrue (length (which (is.na (all.types))) < 12) # got most of them.
} # test.guessProteinIdentifierType
#------------------------------------------------------------------------------------------------------------------------
test.normalizeMatrices = function (matrices)
{
print ('--- test.normalizeMatrices')
colsums = as.integer (sapply (matrices, function (mtx) as.integer (mean (round (colSums (mtx))))))
#checkTrue (all (colsums > 1))
matrices.norm = normalizeMatrices (matrices)
colsums = as.integer (sapply (matrices.norm, function (mtx) as.integer (mean (round (colSums (mtx))))))
checkTrue (all (colsums == 1))
invisible (matrices.norm)
} # test.normalizeMatrices
#------------------------------------------------------------------------------------------------------------------------
test.assignGeneId = function (proteinId)
{
print ('--- test.assignGeneId')
uniprot.ids = c ('Q9GRA5', 'P31314', 'AAC18941', 'O49397')
refseq.ids = c ('NP_995315.1', 'NP_032840', 'NP_599022')
yeast.ids = c ('YKL112W', 'YMR072W', 'YLR131C')
checkEquals (assignGeneId ('NP_995315.1'), list (geneId='4782', type='ENTREZ'))
checkEquals (assignGeneId ('NP_599022'), list (geneId='6095', type='ENTREZ'))
checkEquals (assignGeneId ('P31314'), list (geneId='3195', type='ENTREZ'))
checkEquals (assignGeneId ('YKL112W'), list (geneId='YKL112W', type='SGD'))
# see how successful this is over all 513 proteinIds
tbl.anno = createAnnotationTable ()
mtx.geneId = as.data.frame (t (sapply (tbl.anno$proteinID, assignGeneId)))
tbl.types = as.data.frame (table (as.character (mtx.geneId$type), useNA='always'), stringsAsFactors=FALSE)
checkEquals (tbl.types$Var1, c ("ENTREZ", "SGD", NA))
checkEquals (tbl.types$Freq, c (141, 177, 195))
} # test.assignGeneId
#------------------------------------------------------------------------------------------------------------------------
test.parsePwm = function ()
{
print ('--- test.parsePwm')
lines = c ('UW.Motif.0006 aggaaatg',
'0.890585 0.007855 0.051323 0.050237',
'0.060732 0.004506 0.894170 0.040593',
'0.072765 0.037935 0.860704 0.028596',
'0.929585 0.024037 0.034914 0.011464',
'0.931220 0.023231 0.029078 0.016471',
'0.857934 0.044211 0.072594 0.025261',
'0.065840 0.013777 0.058013 0.862370',
'0.049937 0.036238 0.861871 0.051953')
m6 = parsePwm (lines)
checkEquals (names (m6), c ("title", "consensus.sequence", "matrix"))
pwm = m6$matrix
checkEquals (dim (pwm), c (4, 8))
checkEquals (rownames (pwm), c ('A', 'C', 'G', 'T'))
invisible (m6)
} # test.parsePwm
#------------------------------------------------------------------------------------------------------------------------
