Nothing
inst/unitTests/test_IDMapper.R
In PSICQUIC: Proteomics Standard Initiative Common QUery InterfaCe
# test_IDMapper.R
#-------------------------------------------------------------------------------
# move these to paulsTests when development slows
library(PSICQUIC)
library(RUnit)
library(org.Hs.eg.db)
#-------------------------------------------------------------------------------
if(!exists("mapper"))
mapper <- IDMapper("9606")
#-------------------------------------------------------------------------------
# biomaRt can be flakey. before doing any tests, make sure we can get
# the mart and dataset we need. this is called out of many of the test
# functions found below, and the test proceeds only if it returns TRUE
good.hsapiens.mart.exists <- function(mart.name="ensembl",
desired.dataset="hsapiens_gene_ensembl")
{
if(exists("mart")){
if(mart@biomart == "ENSEMBL_MART_ENSEMBL" & mart@dataset == desired.dataset)
return(TRUE)
}
# otherwise, create a new instance
test.mart <- tryCatch({
useMart(biomart=mart.name)},
error=function(err) NULL)
if(is.null(test.mart))
return(FALSE)
if(desired.dataset %in% listDatasets(test.mart)$dataset)
test.mart <- tryCatch({
useMart(biomart="ensembl", dataset=desired.dataset)},
error=function(err) NULL)
if(!is.null(test.mart)) mart <<- test.mart
return(!is.null(mart))
} # good.hssapiens.mart.exists
#--------------------------------------------------------------------------------
# for use in a few functions below.
# this data.frame ("tbl.myc") was created via
# tbl.myc <- interactions(psicquicServer, "Myc", source="BioGrid", organism="9606")
sample.interactions.filename <- system.file(package="PSICQUIC",
"extdata",
"mycInteractions.RData")
load(sample.interactions.filename)
#-------------------------------------------------------------------------------
paulsTests <- function()
{
test_ctor()
test_.categorize()
test_.translate.uniprotkb()
test_.translate.string()
test_.translate.ensemblGene()
test_.translate.ensemblProt()
test_.translate.locuslink()
test_.translate.refseq()
test_.translateAll()
test_addGeneInfo()
test_preserveKnownGeneIdentifiers()
#test_addStandardNames()
#test_preservePreviouslyAssignedStandardNames()
} # paulsTests
#-------------------------------------------------------------------------------
sampleIDs <- function()
{
c("uniprotkb:P51532",
"entrez gene/locuslink:6597|BIOGRID:112481",
"string:9606.ENSP00000223500|uniprotkb:Q9Y323",
"refseq:NP_001167455",
"ensembl:ENSG00000104765",
#"ensembl:ENSP00000350720",
"ensembl:ENSP00000257290",
"uniprotkb:P34896" # maps to two geneIDs, we want the lesser
)
} # samples
#-------------------------------------------------------------------------------
test_ctor <- function()
{
print("--- test_ctor")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return(TRUE)
}
human <- "9606"
rawIDs <- sampleIDs()
mapper <- IDMapper(human)
checkException(IDMapper("intentional error"))
} # test_ctor
#-------------------------------------------------------------------------------
test_.categorize <- function()
{
print("--- test_.categorize")
rawIDs <- sampleIDs()
x <- PSICQUIC:::.categorize(rawIDs)
categories <- sort(names(x))
checkEquals(categories,
c("ensemblGene", "ensemblProt", "locuslink", "refseq", "string",
"uniprotkb", "unrecognized"))
checkEquals(sapply(x, length),
c(ensemblGene=1L,
ensemblProt=1L,
locuslink=1L,
refseq=1L,
string=1L,
uniprotkb=2L,
unrecognized=0L))
} # test_.categorize
#-------------------------------------------------------------------------------
# uniprotkb:P04637
test_.translate.uniprotkb <- function()
{
print("--- test_.translate.uniprotkb")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
#browser()
#if(!exists("mart")){
# mapper <- IDMapper("9606")
# mart <<- mapper@mart
# }
x <- PSICQUIC:::.categorize(rawIDs)$uniprotkb
checkEquals(length(x), 2)
tbl.x <- PSICQUIC:::.translate.uniprotkb(mart, x)
checkEquals(ncol(tbl.x), 4)
# sometimes multiple hits. note extra geneID.
checkTrue(nrow(tbl.x) >= 2)
# id geneID symbol raw.id
# 1 P34896 102466733 SHMT1 uniprotkb:P34896
# 2 P34896 6470 SHMT1 uniprotkb:P34896
# 3 P51532 6597 SMARCA4 uniprotkb:P51532
row.1 <- match("6470", tbl.x$geneID)
row.2 <- match("6597", tbl.x$geneID)
checkEquals(as.list(tbl.x[row.1,]),
list(id="P34896", geneID="6470", symbol="SHMT1", raw.id="uniprotkb:P34896"))
checkEquals(as.list(tbl.x[row.2,]),
list(id="P51532", geneID="6597", symbol="SMARCA4", raw.id="uniprotkb:P51532"))
} # test_.translate.uniprotkb
#-------------------------------------------------------------------------------
test_.translate.string <- function()
{
print("--- test_.translate.string")
rawIDs <- sampleIDs()
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$string
tbl.x <- PSICQUIC:::.translate.string(mart, x)
checkEquals(tbl.x, data.frame(id="ENSP00000223500",
geneID="51510",
symbol="CHMP5",
raw.id="string:9606.ENSP00000223500|uniprotkb:Q9Y323",
stringsAsFactors=FALSE))
} # test_.translate.uniprotkb
#-------------------------------------------------------------------------------
test_.translate.ensemblGene <- function()
{
print("--- test_.translate.ensemblGene")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$ensemblGene
tbl.x <- PSICQUIC:::.translate.ensemblGene(mart, x)
checkEquals(tbl.x, data.frame(id="ENSG00000104765",
geneID="665",
symbol="BNIP3L",
raw.id="ensembl:ENSG00000104765",
stringsAsFactors=FALSE))
} # test_.translate.ensemblGene
#-------------------------------------------------------------------------------
test_.translate.ensemblProt <- function()
{
print("--- test_.translate.ensemblProt")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$ensemblProt
tbl.x <- PSICQUIC:::.translate.ensemblProt(mart, x)
checkEquals(tbl.x, data.frame(id="ENSP00000257290",
geneID="5156",
symbol="PDGFRA",
raw.id="ensembl:ENSP00000257290",
stringsAsFactors=FALSE))
} # test_.translate.ensemblProt
#-------------------------------------------------------------------------------
test_.translate.locuslink <- function()
{
print("--- test_.translate.locuslink")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$locuslink
tbl.x <- PSICQUIC:::.translate.locuslink(mart, x)
checkEquals(tbl.x, data.frame(id=6597,
geneID="6597",
symbol="SMARCA4",
raw.id="entrez gene/locuslink:6597|BIOGRID:112481",
stringsAsFactors=FALSE))
} # test_.translate.locuslink
#-------------------------------------------------------------------------------
test_.translate.refseq <- function()
{
print("--- test_.translate.refseq")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$refseq
tbl.x <- PSICQUIC:::.translate.refseq(mart, x)
checkEquals(tbl.x, data.frame(id="NP_001167455",
geneID="29117",
symbol="BRD7",
raw.id="refseq:NP_001167455",
stringsAsFactors=FALSE))
} # test_.translate.refseq
#-------------------------------------------------------------------------------
test_.translateAll <- function()
{
print("--- test_translateAll")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
raw.ids <- unique(c(tbl.myc$A, tbl.myc$B))
tbl.ids <- PSICQUIC:::.translateAll(mart, raw.ids)
checkEquals(colnames(tbl.ids), c("id", "geneID", "symbol", "raw.id"))
# sometimes we see off-by-one. be extremely generous, allow for off by 100
# meaning that this test is one for basic function, no longer for
# precise mapping
inexactitude.margin <- 100
expected.min <- length(raw.ids) - inexactitude.margin
expected.max <- length(raw.ids) + inexactitude.margin
expected.range <- expected.min:expected.max
checkTrue(nrow(tbl.ids) %in% expected.range)
} # test_.translateAll
#-------------------------------------------------------------------------------
test_addGeneInfo <- function()
{
print("--- test_addGeneInfo")
human <- "9606"
if(!exists("mapper"))
mapper <<- IDMapper(human)
tbl.mycAugmented <- addGeneInfo(mapper, tbl.myc)
checkEquals(dim(tbl.mycAugmented), c(nrow(tbl.myc), ncol(tbl.myc) + 4))
checkTrue(all(sapply(tbl.mycAugmented,function(column) !is.factor(column))))
} # test_addGeneInfo
#-------------------------------------------------------------------------------
test_addGeneInfoMinimalTable <- function()
{
print("--- test_addGeneInfoMinimalTable")
mapper <- IDMapper("9606")
tbl <- data.frame(A="entrez gene/locuslink:238|BIOGRID:106739",
B="entrez gene/locuslink:3718|BIOGRID:109921",
stringsAsFactors=FALSE)
tbl.withGeneInfo <- addGeneInfo(mapper, tbl)
checkEquals(dim(tbl.withGeneInfo), c (1, 6))
} # test_addGeneInfoMinimalTable
#-------------------------------------------------------------------------------
# take a row from the RefNet gerstein.2012 interactions, which already has
# gene symbols and geneIDs, and ensure that the IDMapper leaves them intact
test_preserveKnownGeneIdentifiers <- function()
{
print("--- test_preserveKnownGeneIdentifiers")
row.1 <- list(A="MYC",
B="SHMT1",
altA="4609",
altB="6470",
aliasA="MYC",
aliasB="SHMT1",
detectionMethod="psi-mi:MI:0402(chromatin immunoprecipitation assay)",
firstAuthor="-",
publicationID="gerstein.2012",
taxonA="9606",
taxonB="9606",
type="psi-mi:MI:0407(direct interaction)",
sourceDatabases="gerstein.2012",
interactionID="-",
confidenceScore="-",
provider="gerstein.2012",
A.name="MYC",
B.name="SHMT1",
A.id="4609",
B.id="6470")
row.2 <- list(A="uniprotkb:Q9GZQ8",
B="uniprotkb:P34896",
altA="intact:EBI-373144|uniprotkb:Q6NW02",
altB="intact:EBI-715117|uniprotkb:D3DXD0|uniprotkb:Q9UMD1|uniprotkb:Q9UMD2|uniprotkb:Q96HY0",
aliasA="psi-mi:mlp3b_human(display_long)|uniprotkb:MAP1LC3B(gene name)|psi-mi:MAP1LC3B(display_short)|uniprotkb:MAP1ALC3(gene name synonym)|uniprotkb:Microtubule-associated protein 1 light chain 3 beta(gene name synonym)|uniprotkb:MAP1A/MAP1B light chain 3 B(gene name synonym)|uniprotkb:MAP1 light chain 3-like protein 2(gene name synonym)|uniprotkb:Autophagy-related protein LC3 B(gene name synonym)|uniprotkb:Autophagy-related ubiquitin-like modifier LC3 B(gene name synonym)",
aliasB="psi-mi:glyc_human(display_long)|uniprotkb:Glycine hydroxymethyltransferase(gene name synonym)|uniprotkb:SHMT1(gene name)|psi-mi:SHMT1(display_short)|uniprotkb:Serine methylase(gene name synonym)",
detectionMethod="psi-mi:MI:0007(anti tag coimmunoprecipitation)",
firstAuthor="Behrends et al. (2010)",
publicationID="pubmed:20562859|imex:IM-15184",
taxonA="taxid:9606(human)|taxid:9606(Homo sapiens)",
taxonB="taxid:9606(human)|taxid:9606(Homo sapiens)",
type="psi-mi:MI:0914(association)",
sourceDatabases="psi-mi:MI:0469(IntAct)",
interactionID="intact:EBI-3045543|imex:IM-15184-337",
confidenceScore="intact-miscore:0.35",
provider="IntAct")
row.3 <- list(A="_6470_1_c",
B="R_GHMT2r",
altA="6470",
altB="-",
aliasA="SHMT1",
aliasB="glycine hydroxymethyltransferase, reversible",
detectionMethod="psi-mi:MI:0046(experimental knowledge based)",
firstAuthor="-",
publicationID="9038835",
taxonA="9606",
taxonB="9606",
type="modifies",
sourceDatabases="recon2",
interactionID="-",
confidenceScore="-",
provider="recon2",
A.name="-",
B.name="-",
A.id="-",
B.id="-",
compartment="c",
a.uniprot="P34896",
a.sboTerm="SBO:0000252",
a.chebi="-",
a.kegg.compound="-",
a.kegg.genes="hsa:6470",
a.kegg.drug="-",
a.hmdb="-",
a.pubchem.substance="-",
reversible="true")
tbl.1 <- as.data.frame(row.1, stringsAsFactors=FALSE)
tbl.2 <- as.data.frame(row.2, stringsAsFactors=FALSE)
tbl.3 <- as.data.frame(row.3, stringsAsFactors=FALSE)
# used to use my improvised RefNet:::.smartRbind at this
# point, to create a single data.frame with all columns.
# found in the three lists/data.frames hand-crafted above.
# this introduces a RefNet dependency into the PSICQUIC
# package, clearly undesirable: RefNet depends upon PSICQUIC
#
# so now using hadley's rbind.fill instead, arguably a better
# choice anyway. one difference must be accomodated:
# rbind.fill sensibly inserts NAs in empty cells; smartRbind
# uses "-" since that is PSICQUIC's token for missing values.
# we take that extra step below
#tbl <- RefNet:::.smartRbind(tbl.1, tbl.2)
#tbl <- RefNet:::.smartRbind(tbl, tbl.3)
tbl <- rbind.fill(tbl.1, tbl.2)
tbl <- rbind.fill(tbl, tbl.3)
cols <- colnames(tbl)
for(col in cols){
column.as.list <- tbl[, col]
na.entries <- which (is.na(column.as.list))
#printf("%d na.entries in col %s", length(na.entries), col)
if(length(na.entries) > 0)
tbl[na.entries, col] <- "-"
} # for col
tbl.mapped <- addGeneInfo(mapper, tbl)
checkIdentical(tbl.1, tbl.mapped[1,1:20])
# second row of returned tbl.mapped should match incoming tbl.2, up to the 16th column
checkIdentical(as.list(tbl[2,1:16]), as.list(tbl.2))
# the last 4 columns should have these identifiers
checkEquals(as.list(tbl.mapped[2,17:20]), list(A.name="MAP1LC3B",
B.name="SHMT1",
A.id="81631",
B.id="6470"))
# row 3 should not change at all. the interactors are
# a recon2 interaction
# a recon2 modifier, which comes in a form we do not yet
# translate into standard forms
checkTrue(all(tbl.mapped[3,] == tbl.3))
x <- 99
} # test_preserveKnownGeneIdentifiers
#-------------------------------------------------------------------------------
test_addStandardNames <- function()
{
print("--- test_addStandardNames")
human <- "9606"
if(!exists("mapper"))
mapper <<- IDMapper(human)
# work with just the first 10 interactions in the table
max <- 10
tbl.mycAugmented <- addStandardNames(mapper, tbl.myc[1:max,])
checkEquals(dim(tbl.mycAugmented), c(max, ncol(tbl.myc) + 4))
checkEquals(colnames(tbl.mycAugmented)[17:20],
c("A.name", "B.name", "A.id", "B.id"))
checkTrue(all(sapply(tbl.mycAugmented,function(column) !is.factor(column))))
geneIds <- with(tbl.mycAugmented, sort(unique(c(A.id, B.id))))
geneSyms <- with(tbl.mycAugmented, sort(unique(c(A.name, B.name))))
checkEquals(geneIds, c("10273", "4609", "5204", "5300", "672", "7316", "8841" ))
checkEquals(sort(as.character(mget(geneIds, org.Hs.egSYMBOL))), geneSyms)
} # test_addStandardNames
#-------------------------------------------------------------------------------
# take a row from the RefNet gerstein.2012 interactions, which already has
# gene symbols and geneIDs, and ensure that the IDMapper leaves them intact
no_test_preservePreviouslyAssignedStandardNames <- function()
{
print("--- test_preservePreviouslyAssignedStandardNames")
row.1 <- list(A="MYC",
B="SHMT1",
altA="4609",
altB="6470",
aliasA="MYC",
aliasB="SHMT1",
detectionMethod="psi-mi:MI:0402(chromatin immunoprecipitation assay)",
firstAuthor="-",
publicationID="gerstein.2012",
taxonA="9606",
taxonB="9606",
type="psi-mi:MI:0407(direct interaction)",
sourceDatabases="gerstein.2012",
interactionID="-",
confidenceScore="-",
provider="gerstein.2012",
A.name="MYC",
B.name="SHMT1",
A.id="4609",
B.id="6470")
row.2 <- list(A="uniprotkb:Q9GZQ8",
B="uniprotkb:P34896",
altA="intact:EBI-373144|uniprotkb:Q6NW02",
altB="intact:EBI-715117|uniprotkb:D3DXD0|uniprotkb:Q9UMD1|uniprotkb:Q9UMD2|uniprotkb:Q96HY0",
aliasA="psi-mi:mlp3b_human(display_long)|uniprotkb:MAP1LC3B(gene name)|psi-mi:MAP1LC3B(display_short)|uniprotkb:MAP1ALC3(gene name synonym)|uniprotkb:Microtubule-associated protein 1 light chain 3 beta(gene name synonym)|uniprotkb:MAP1A/MAP1B light chain 3 B(gene name synonym)|uniprotkb:MAP1 light chain 3-like protein 2(gene name synonym)|uniprotkb:Autophagy-related protein LC3 B(gene name synonym)|uniprotkb:Autophagy-related ubiquitin-like modifier LC3 B(gene name synonym)",
aliasB="psi-mi:glyc_human(display_long)|uniprotkb:Glycine hydroxymethyltransferase(gene name synonym)|uniprotkb:SHMT1(gene name)|psi-mi:SHMT1(display_short)|uniprotkb:Serine methylase(gene name synonym)",
detectionMethod="psi-mi:MI:0007(anti tag coimmunoprecipitation)",
firstAuthor="Behrends et al. (2010)",
publicationID="pubmed:20562859|imex:IM-15184",
taxonA="taxid:9606(human)|taxid:9606(Homo sapiens)",
taxonB="taxid:9606(human)|taxid:9606(Homo sapiens)",
type="psi-mi:MI:0914(association)",
sourceDatabases="psi-mi:MI:0469(IntAct)",
interactionID="intact:EBI-3045543|imex:IM-15184-337",
confidenceScore="intact-miscore:0.35",
provider="IntAct")
row.3 <- list(A="_6470_1_c",
B="R_GHMT2r",
altA="6470",
altB="-",
aliasA="SHMT1",
aliasB="glycine hydroxymethyltransferase, reversible",
detectionMethod="psi-mi:MI:0046(experimental knowledge based)",
firstAuthor="-",
publicationID="9038835",
taxonA="9606",
taxonB="9606",
type="modifies",
sourceDatabases="recon2",
interactionID="-",
confidenceScore="-",
provider="recon2",
A.name="-",
B.name="-",
A.id="-",
B.id="-",
compartment="c",
a.uniprot="P34896",
a.sboTerm="SBO:0000252",
a.chebi="-",
a.kegg.compound="-",
a.kegg.genes="hsa:6470",
a.kegg.drug="-",
a.hmdb="-",
a.pubchem.substance="-",
reversible="true")
tbl.1 <- as.data.frame(row.1, stringsAsFactors=FALSE)
tbl.2 <- as.data.frame(row.2, stringsAsFactors=FALSE)
tbl.3 <- as.data.frame(row.3, stringsAsFactors=FALSE)
tbl <- RefNet:::.smartRbind(tbl.1, tbl.2)
tbl <- RefNet:::.smartRbind(tbl, tbl.3)
tbl.mapped <- addStandardNames(mapper, tbl)
checkIdentical(tbl.1, tbl.mapped[1,1:20])
# second row of returned tbl.mapped should match incoming tbl.2, up to the 16th column
checkIdentical(as.list(tbl[2,1:16]), as.list(tbl.2))
# the last 4 columns should have these identifiers
checkEquals(as.list(tbl.mapped[2,17:20]), list(A.name="MAP1LC3B",
B.name="SHMT1",
A.id="81631",
B.id="6470"))
# row 3 should not change at all. the interactors are
# a recon2 interaction
# a recon2 modifier, which comes in a form we do not yet
# translate into standard forms
checkTrue(all(tbl.mapped[3,] == tbl.3))
x <- 99
} # test_preservePreviouslyAssignedStandardNames
#-------------------------------------------------------------------------------
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# test_IDMapper.R
#-------------------------------------------------------------------------------
# move these to paulsTests when development slows
library(PSICQUIC)
library(RUnit)
library(org.Hs.eg.db)
#-------------------------------------------------------------------------------
if(!exists("mapper"))
mapper <- IDMapper("9606")
#-------------------------------------------------------------------------------
# biomaRt can be flakey. before doing any tests, make sure we can get
# the mart and dataset we need. this is called out of many of the test
# functions found below, and the test proceeds only if it returns TRUE
good.hsapiens.mart.exists <- function(mart.name="ensembl",
desired.dataset="hsapiens_gene_ensembl")
{
if(exists("mart")){
if(mart@biomart == "ENSEMBL_MART_ENSEMBL" & mart@dataset == desired.dataset)
return(TRUE)
}
# otherwise, create a new instance
test.mart <- tryCatch({
useMart(biomart=mart.name)},
error=function(err) NULL)
if(is.null(test.mart))
return(FALSE)
if(desired.dataset %in% listDatasets(test.mart)$dataset)
test.mart <- tryCatch({
useMart(biomart="ensembl", dataset=desired.dataset)},
error=function(err) NULL)
if(!is.null(test.mart)) mart <<- test.mart
return(!is.null(mart))
} # good.hssapiens.mart.exists
#--------------------------------------------------------------------------------
# for use in a few functions below.
# this data.frame ("tbl.myc") was created via
# tbl.myc <- interactions(psicquicServer, "Myc", source="BioGrid", organism="9606")
sample.interactions.filename <- system.file(package="PSICQUIC",
"extdata",
"mycInteractions.RData")
load(sample.interactions.filename)
#-------------------------------------------------------------------------------
paulsTests <- function()
{
test_ctor()
test_.categorize()
test_.translate.uniprotkb()
test_.translate.string()
test_.translate.ensemblGene()
test_.translate.ensemblProt()
test_.translate.locuslink()
test_.translate.refseq()
test_.translateAll()
test_addGeneInfo()
test_preserveKnownGeneIdentifiers()
#test_addStandardNames()
#test_preservePreviouslyAssignedStandardNames()
} # paulsTests
#-------------------------------------------------------------------------------
sampleIDs <- function()
{
c("uniprotkb:P51532",
"entrez gene/locuslink:6597|BIOGRID:112481",
"string:9606.ENSP00000223500|uniprotkb:Q9Y323",
"refseq:NP_001167455",
"ensembl:ENSG00000104765",
#"ensembl:ENSP00000350720",
"ensembl:ENSP00000257290",
"uniprotkb:P34896" # maps to two geneIDs, we want the lesser
)
} # samples
#-------------------------------------------------------------------------------
test_ctor <- function()
{
print("--- test_ctor")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return(TRUE)
}
human <- "9606"
rawIDs <- sampleIDs()
mapper <- IDMapper(human)
checkException(IDMapper("intentional error"))
} # test_ctor
#-------------------------------------------------------------------------------
test_.categorize <- function()
{
print("--- test_.categorize")
rawIDs <- sampleIDs()
x <- PSICQUIC:::.categorize(rawIDs)
categories <- sort(names(x))
checkEquals(categories,
c("ensemblGene", "ensemblProt", "locuslink", "refseq", "string",
"uniprotkb", "unrecognized"))
checkEquals(sapply(x, length),
c(ensemblGene=1L,
ensemblProt=1L,
locuslink=1L,
refseq=1L,
string=1L,
uniprotkb=2L,
unrecognized=0L))
} # test_.categorize
#-------------------------------------------------------------------------------
# uniprotkb:P04637
test_.translate.uniprotkb <- function()
{
print("--- test_.translate.uniprotkb")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
#browser()
#if(!exists("mart")){
# mapper <- IDMapper("9606")
# mart <<- mapper@mart
# }
x <- PSICQUIC:::.categorize(rawIDs)$uniprotkb
checkEquals(length(x), 2)
tbl.x <- PSICQUIC:::.translate.uniprotkb(mart, x)
checkEquals(ncol(tbl.x), 4)
# sometimes multiple hits. note extra geneID.
checkTrue(nrow(tbl.x) >= 2)
# id geneID symbol raw.id
# 1 P34896 102466733 SHMT1 uniprotkb:P34896
# 2 P34896 6470 SHMT1 uniprotkb:P34896
# 3 P51532 6597 SMARCA4 uniprotkb:P51532
row.1 <- match("6470", tbl.x$geneID)
row.2 <- match("6597", tbl.x$geneID)
checkEquals(as.list(tbl.x[row.1,]),
list(id="P34896", geneID="6470", symbol="SHMT1", raw.id="uniprotkb:P34896"))
checkEquals(as.list(tbl.x[row.2,]),
list(id="P51532", geneID="6597", symbol="SMARCA4", raw.id="uniprotkb:P51532"))
} # test_.translate.uniprotkb
#-------------------------------------------------------------------------------
test_.translate.string <- function()
{
print("--- test_.translate.string")
rawIDs <- sampleIDs()
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$string
tbl.x <- PSICQUIC:::.translate.string(mart, x)
checkEquals(tbl.x, data.frame(id="ENSP00000223500",
geneID="51510",
symbol="CHMP5",
raw.id="string:9606.ENSP00000223500|uniprotkb:Q9Y323",
stringsAsFactors=FALSE))
} # test_.translate.uniprotkb
#-------------------------------------------------------------------------------
test_.translate.ensemblGene <- function()
{
print("--- test_.translate.ensemblGene")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$ensemblGene
tbl.x <- PSICQUIC:::.translate.ensemblGene(mart, x)
checkEquals(tbl.x, data.frame(id="ENSG00000104765",
geneID="665",
symbol="BNIP3L",
raw.id="ensembl:ENSG00000104765",
stringsAsFactors=FALSE))
} # test_.translate.ensemblGene
#-------------------------------------------------------------------------------
test_.translate.ensemblProt <- function()
{
print("--- test_.translate.ensemblProt")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$ensemblProt
tbl.x <- PSICQUIC:::.translate.ensemblProt(mart, x)
checkEquals(tbl.x, data.frame(id="ENSP00000257290",
geneID="5156",
symbol="PDGFRA",
raw.id="ensembl:ENSP00000257290",
stringsAsFactors=FALSE))
} # test_.translate.ensemblProt
#-------------------------------------------------------------------------------
test_.translate.locuslink <- function()
{
print("--- test_.translate.locuslink")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$locuslink
tbl.x <- PSICQUIC:::.translate.locuslink(mart, x)
checkEquals(tbl.x, data.frame(id=6597,
geneID="6597",
symbol="SMARCA4",
raw.id="entrez gene/locuslink:6597|BIOGRID:112481",
stringsAsFactors=FALSE))
} # test_.translate.locuslink
#-------------------------------------------------------------------------------
test_.translate.refseq <- function()
{
print("--- test_.translate.refseq")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
rawIDs <- sampleIDs()
if(!exists("mart")){
#mapper <- IDMapper("9606", rawIDs)
mapper <- IDMapper("9606")
mart <<- mapper@mart
}
x <- PSICQUIC:::.categorize(rawIDs)$refseq
tbl.x <- PSICQUIC:::.translate.refseq(mart, x)
checkEquals(tbl.x, data.frame(id="NP_001167455",
geneID="29117",
symbol="BRD7",
raw.id="refseq:NP_001167455",
stringsAsFactors=FALSE))
} # test_.translate.refseq
#-------------------------------------------------------------------------------
test_.translateAll <- function()
{
print("--- test_translateAll")
if(!good.hsapiens.mart.exists()) {
message("cannot create biomart, skipping test")
return
}
raw.ids <- unique(c(tbl.myc$A, tbl.myc$B))
tbl.ids <- PSICQUIC:::.translateAll(mart, raw.ids)
checkEquals(colnames(tbl.ids), c("id", "geneID", "symbol", "raw.id"))
# sometimes we see off-by-one. be extremely generous, allow for off by 100
# meaning that this test is one for basic function, no longer for
# precise mapping
inexactitude.margin <- 100
expected.min <- length(raw.ids) - inexactitude.margin
expected.max <- length(raw.ids) + inexactitude.margin
expected.range <- expected.min:expected.max
checkTrue(nrow(tbl.ids) %in% expected.range)
} # test_.translateAll
#-------------------------------------------------------------------------------
test_addGeneInfo <- function()
{
print("--- test_addGeneInfo")
human <- "9606"
if(!exists("mapper"))
mapper <<- IDMapper(human)
tbl.mycAugmented <- addGeneInfo(mapper, tbl.myc)
checkEquals(dim(tbl.mycAugmented), c(nrow(tbl.myc), ncol(tbl.myc) + 4))
checkTrue(all(sapply(tbl.mycAugmented,function(column) !is.factor(column))))
} # test_addGeneInfo
#-------------------------------------------------------------------------------
test_addGeneInfoMinimalTable <- function()
{
print("--- test_addGeneInfoMinimalTable")
mapper <- IDMapper("9606")
tbl <- data.frame(A="entrez gene/locuslink:238|BIOGRID:106739",
B="entrez gene/locuslink:3718|BIOGRID:109921",
stringsAsFactors=FALSE)
tbl.withGeneInfo <- addGeneInfo(mapper, tbl)
checkEquals(dim(tbl.withGeneInfo), c (1, 6))
} # test_addGeneInfoMinimalTable
#-------------------------------------------------------------------------------
# take a row from the RefNet gerstein.2012 interactions, which already has
# gene symbols and geneIDs, and ensure that the IDMapper leaves them intact
test_preserveKnownGeneIdentifiers <- function()
{
print("--- test_preserveKnownGeneIdentifiers")
row.1 <- list(A="MYC",
B="SHMT1",
altA="4609",
altB="6470",
aliasA="MYC",
aliasB="SHMT1",
detectionMethod="psi-mi:MI:0402(chromatin immunoprecipitation assay)",
firstAuthor="-",
publicationID="gerstein.2012",
taxonA="9606",
taxonB="9606",
type="psi-mi:MI:0407(direct interaction)",
sourceDatabases="gerstein.2012",
interactionID="-",
confidenceScore="-",
provider="gerstein.2012",
A.name="MYC",
B.name="SHMT1",
A.id="4609",
B.id="6470")
row.2 <- list(A="uniprotkb:Q9GZQ8",
B="uniprotkb:P34896",
altA="intact:EBI-373144|uniprotkb:Q6NW02",
altB="intact:EBI-715117|uniprotkb:D3DXD0|uniprotkb:Q9UMD1|uniprotkb:Q9UMD2|uniprotkb:Q96HY0",
aliasA="psi-mi:mlp3b_human(display_long)|uniprotkb:MAP1LC3B(gene name)|psi-mi:MAP1LC3B(display_short)|uniprotkb:MAP1ALC3(gene name synonym)|uniprotkb:Microtubule-associated protein 1 light chain 3 beta(gene name synonym)|uniprotkb:MAP1A/MAP1B light chain 3 B(gene name synonym)|uniprotkb:MAP1 light chain 3-like protein 2(gene name synonym)|uniprotkb:Autophagy-related protein LC3 B(gene name synonym)|uniprotkb:Autophagy-related ubiquitin-like modifier LC3 B(gene name synonym)",
aliasB="psi-mi:glyc_human(display_long)|uniprotkb:Glycine hydroxymethyltransferase(gene name synonym)|uniprotkb:SHMT1(gene name)|psi-mi:SHMT1(display_short)|uniprotkb:Serine methylase(gene name synonym)",
detectionMethod="psi-mi:MI:0007(anti tag coimmunoprecipitation)",
firstAuthor="Behrends et al. (2010)",
publicationID="pubmed:20562859|imex:IM-15184",
taxonA="taxid:9606(human)|taxid:9606(Homo sapiens)",
taxonB="taxid:9606(human)|taxid:9606(Homo sapiens)",
type="psi-mi:MI:0914(association)",
sourceDatabases="psi-mi:MI:0469(IntAct)",
interactionID="intact:EBI-3045543|imex:IM-15184-337",
confidenceScore="intact-miscore:0.35",
provider="IntAct")
row.3 <- list(A="_6470_1_c",
B="R_GHMT2r",
altA="6470",
altB="-",
aliasA="SHMT1",
aliasB="glycine hydroxymethyltransferase, reversible",
detectionMethod="psi-mi:MI:0046(experimental knowledge based)",
firstAuthor="-",
publicationID="9038835",
taxonA="9606",
taxonB="9606",
type="modifies",
sourceDatabases="recon2",
interactionID="-",
confidenceScore="-",
provider="recon2",
A.name="-",
B.name="-",
A.id="-",
B.id="-",
compartment="c",
a.uniprot="P34896",
a.sboTerm="SBO:0000252",
a.chebi="-",
a.kegg.compound="-",
a.kegg.genes="hsa:6470",
a.kegg.drug="-",
a.hmdb="-",
a.pubchem.substance="-",
reversible="true")
tbl.1 <- as.data.frame(row.1, stringsAsFactors=FALSE)
tbl.2 <- as.data.frame(row.2, stringsAsFactors=FALSE)
tbl.3 <- as.data.frame(row.3, stringsAsFactors=FALSE)
# used to use my improvised RefNet:::.smartRbind at this
# point, to create a single data.frame with all columns.
# found in the three lists/data.frames hand-crafted above.
# this introduces a RefNet dependency into the PSICQUIC
# package, clearly undesirable: RefNet depends upon PSICQUIC
#
# so now using hadley's rbind.fill instead, arguably a better
# choice anyway. one difference must be accomodated:
# rbind.fill sensibly inserts NAs in empty cells; smartRbind
# uses "-" since that is PSICQUIC's token for missing values.
# we take that extra step below
#tbl <- RefNet:::.smartRbind(tbl.1, tbl.2)
#tbl <- RefNet:::.smartRbind(tbl, tbl.3)
tbl <- rbind.fill(tbl.1, tbl.2)
tbl <- rbind.fill(tbl, tbl.3)
cols <- colnames(tbl)
for(col in cols){
column.as.list <- tbl[, col]
na.entries <- which (is.na(column.as.list))
#printf("%d na.entries in col %s", length(na.entries), col)
if(length(na.entries) > 0)
tbl[na.entries, col] <- "-"
} # for col
tbl.mapped <- addGeneInfo(mapper, tbl)
checkIdentical(tbl.1, tbl.mapped[1,1:20])
# second row of returned tbl.mapped should match incoming tbl.2, up to the 16th column
checkIdentical(as.list(tbl[2,1:16]), as.list(tbl.2))
# the last 4 columns should have these identifiers
checkEquals(as.list(tbl.mapped[2,17:20]), list(A.name="MAP1LC3B",
B.name="SHMT1",
A.id="81631",
B.id="6470"))
# row 3 should not change at all. the interactors are
# a recon2 interaction
# a recon2 modifier, which comes in a form we do not yet
# translate into standard forms
checkTrue(all(tbl.mapped[3,] == tbl.3))
x <- 99
} # test_preserveKnownGeneIdentifiers
#-------------------------------------------------------------------------------
test_addStandardNames <- function()
{
print("--- test_addStandardNames")
human <- "9606"
if(!exists("mapper"))
mapper <<- IDMapper(human)
# work with just the first 10 interactions in the table
max <- 10
tbl.mycAugmented <- addStandardNames(mapper, tbl.myc[1:max,])
checkEquals(dim(tbl.mycAugmented), c(max, ncol(tbl.myc) + 4))
checkEquals(colnames(tbl.mycAugmented)[17:20],
c("A.name", "B.name", "A.id", "B.id"))
checkTrue(all(sapply(tbl.mycAugmented,function(column) !is.factor(column))))
geneIds <- with(tbl.mycAugmented, sort(unique(c(A.id, B.id))))
geneSyms <- with(tbl.mycAugmented, sort(unique(c(A.name, B.name))))
checkEquals(geneIds, c("10273", "4609", "5204", "5300", "672", "7316", "8841" ))
checkEquals(sort(as.character(mget(geneIds, org.Hs.egSYMBOL))), geneSyms)
} # test_addStandardNames
#-------------------------------------------------------------------------------
# take a row from the RefNet gerstein.2012 interactions, which already has
# gene symbols and geneIDs, and ensure that the IDMapper leaves them intact
no_test_preservePreviouslyAssignedStandardNames <- function()
{
print("--- test_preservePreviouslyAssignedStandardNames")
row.1 <- list(A="MYC",
B="SHMT1",
altA="4609",
altB="6470",
aliasA="MYC",
aliasB="SHMT1",
detectionMethod="psi-mi:MI:0402(chromatin immunoprecipitation assay)",
firstAuthor="-",
publicationID="gerstein.2012",
taxonA="9606",
taxonB="9606",
type="psi-mi:MI:0407(direct interaction)",
sourceDatabases="gerstein.2012",
interactionID="-",
confidenceScore="-",
provider="gerstein.2012",
A.name="MYC",
B.name="SHMT1",
A.id="4609",
B.id="6470")
row.2 <- list(A="uniprotkb:Q9GZQ8",
B="uniprotkb:P34896",
altA="intact:EBI-373144|uniprotkb:Q6NW02",
altB="intact:EBI-715117|uniprotkb:D3DXD0|uniprotkb:Q9UMD1|uniprotkb:Q9UMD2|uniprotkb:Q96HY0",
aliasA="psi-mi:mlp3b_human(display_long)|uniprotkb:MAP1LC3B(gene name)|psi-mi:MAP1LC3B(display_short)|uniprotkb:MAP1ALC3(gene name synonym)|uniprotkb:Microtubule-associated protein 1 light chain 3 beta(gene name synonym)|uniprotkb:MAP1A/MAP1B light chain 3 B(gene name synonym)|uniprotkb:MAP1 light chain 3-like protein 2(gene name synonym)|uniprotkb:Autophagy-related protein LC3 B(gene name synonym)|uniprotkb:Autophagy-related ubiquitin-like modifier LC3 B(gene name synonym)",
aliasB="psi-mi:glyc_human(display_long)|uniprotkb:Glycine hydroxymethyltransferase(gene name synonym)|uniprotkb:SHMT1(gene name)|psi-mi:SHMT1(display_short)|uniprotkb:Serine methylase(gene name synonym)",
detectionMethod="psi-mi:MI:0007(anti tag coimmunoprecipitation)",
firstAuthor="Behrends et al. (2010)",
publicationID="pubmed:20562859|imex:IM-15184",
taxonA="taxid:9606(human)|taxid:9606(Homo sapiens)",
taxonB="taxid:9606(human)|taxid:9606(Homo sapiens)",
type="psi-mi:MI:0914(association)",
sourceDatabases="psi-mi:MI:0469(IntAct)",
interactionID="intact:EBI-3045543|imex:IM-15184-337",
confidenceScore="intact-miscore:0.35",
provider="IntAct")
row.3 <- list(A="_6470_1_c",
B="R_GHMT2r",
altA="6470",
altB="-",
aliasA="SHMT1",
aliasB="glycine hydroxymethyltransferase, reversible",
detectionMethod="psi-mi:MI:0046(experimental knowledge based)",
firstAuthor="-",
publicationID="9038835",
taxonA="9606",
taxonB="9606",
type="modifies",
sourceDatabases="recon2",
interactionID="-",
confidenceScore="-",
provider="recon2",
A.name="-",
B.name="-",
A.id="-",
B.id="-",
compartment="c",
a.uniprot="P34896",
a.sboTerm="SBO:0000252",
a.chebi="-",
a.kegg.compound="-",
a.kegg.genes="hsa:6470",
a.kegg.drug="-",
a.hmdb="-",
a.pubchem.substance="-",
reversible="true")
tbl.1 <- as.data.frame(row.1, stringsAsFactors=FALSE)
tbl.2 <- as.data.frame(row.2, stringsAsFactors=FALSE)
tbl.3 <- as.data.frame(row.3, stringsAsFactors=FALSE)
tbl <- RefNet:::.smartRbind(tbl.1, tbl.2)
tbl <- RefNet:::.smartRbind(tbl, tbl.3)
tbl.mapped <- addStandardNames(mapper, tbl)
checkIdentical(tbl.1, tbl.mapped[1,1:20])
# second row of returned tbl.mapped should match incoming tbl.2, up to the 16th column
checkIdentical(as.list(tbl[2,1:16]), as.list(tbl.2))
# the last 4 columns should have these identifiers
checkEquals(as.list(tbl.mapped[2,17:20]), list(A.name="MAP1LC3B",
B.name="SHMT1",
A.id="81631",
B.id="6470"))
# row 3 should not change at all. the interactors are
# a recon2 interaction
# a recon2 modifier, which comes in a form we do not yet
# translate into standard forms
checkTrue(all(tbl.mapped[3,] == tbl.3))
x <- 99
} # test_preservePreviouslyAssignedStandardNames
#-------------------------------------------------------------------------------
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