inst/scripts/import/stamlab/test.R
In PriceLab/MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs
# 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$matrix
checkEquals (dim (pwm), c (4, 8))
checkEquals (rownames (pwm), c ('A', 'C', 'G', 'T'))
invisible (m6)
} # test.parsePwm
#------------------------------------------------------------------------------------------------------------------------
PriceLab/MotifDb documentation built on March 23, 2022, 7:42 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# stamlab/test.R
# notes: 3 matrices come w/o speciesID, tax = 'vertebrates'. not our problem to fix, at least not yet.
# TBP, HNF4A and CEBPA (MA0108.2, MA0114.1, MA0102.2)
#------------------------------------------------------------------------------------------------------------------------
library (RUnit)
#------------------------------------------------------------------------------------------------------------------------
source("import.R")
#------------------------------------------------------------------------------------------------------------------------
run.tests = function (dataDir)
{
dataDir <- file.path(dataDir, "stamlab")
x.rawMatrixList <<- test.readRawMatrices (dataDir)
x.novels <<- test.readNovelStatus (dataDir)
x.matrices <<- test.extractAndNormalizeMatrices (x.rawMatrixList)
x.tbl.md <<- test.createMetadataTable (x.matrices, x.novels)
x.matrices.renamed <<- test.renameMatrices (x.matrices, x.tbl.md)
} # run.tests
#------------------------------------------------------------------------------------------------------------------------
test.readRawMatrices = function (dataDir)
{
print ('--- test.readMatrices')
list.pwms = readRawMatrices (dataDir)
checkEquals (length (list.pwms), 683)
checkEquals (names (list.pwms [[1]]), c ("title", "consensus.sequence", "matrix"))
checkEquals (rownames (list.pwms[[1]]$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
#------------------------------------------------------------------------------------------------------------------------
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.