tests/testthat/test-CNPreprocessing.R
In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events
### Unit tests for CNVMetricsMethods.R functions
library(CNprep)
segExample <- data.frame(ID=c(rep("WZ1", 5)),
start=c(1, 16, 23, 31, 38),
end=c(15, 22, 30, 37, 50),
num.probes=c(15, 7, 8, 720, 518),
seg.median=c(0.047797239, -0.215466818, 0.043107477, -0.225908644,
0.037204403),
chrom=c(rep(1, 5)),
chrom.pos.start=c(932544, 16004440, 38093655, 78729960, 103416416),
chrom.pos.end=c(15844870, 37974708, 78619856, 103394039, 142176090),
cytoband.start=c("p36.33", "p36.13", "p34.3", "p31.1", "p21.1"),
cytoband.end=c("p36.13", "p34.3", "p31.1", "p21.1", "q21.1"),
abs.pos.start=c(932544, 16004440, 38093655, 78729960, 103416416),
abs.pos.end=c(15844870, 37974708, 78619856, 103394039, 142176090))
rateExample <- matrix(data = c(0.0720738404241163, 0.119913919265996, 0.154459489283567, 0.0409946196196852, -0.0828437318817242,
0.0930527245776551, 0.170908929806745, 0.100289489712059, 0.08662475225992, -0.00385501101587094, -0.195791648504205,
0.0636341122831496, 0.109449474459845, 0.043428961427158, 0.160174528536138, 0.0410580626539806, 0.0405224616647681,
0.0986143513758616, 0.0731923745507058, 0.0121261797978406, 0.107795728119586, 0.0832422912347904, 0.0727354592601023,
0.1475937155592, 0.0810554254709479, 0.162564668451733, 0.0590673628590426, -0.0728672744452223, 0.0284354530744622,
0.160126815673499, 0.190799021333644, -0.0269711432208357, 0.0203580612494725, -0.00731229981882388, -0.0440263312613861,
-0.0817496261303279, 0.0146393203392997, 0.0860431917828892, 0.0213604328945665, 0.0789323375946298, 0.0757082196458755,
-0.0507940506094144, 0.0217577735749916, 0.0281455710909498, 0.0196702655955798, 0.154422985605817, 0.260452283950961, 0.122065762785514,
-0.0197506768456278, -0.0277870900508885), ncol = 1)
colnames(rateExample) <- c("WZ1")
normSegs <- matrix(data = c(0.023032697, 0.0069878681, 0.0013329618, 0.0110395179,
0.0007606011, 0.0023178528, -0.0076653454, -0.0044130592,
-0.0044268312, -0.0362319897,
0.0001533229, 0.0075387269, 0.0078903700, 0.0007193940,
0.0011609480, 0.0001808010, -0.0172001485, -0.0034588337,
-0.0064778796, -0.0001113585), ncol = 1)
colnames(normSegs) <- c("segmedian")
normalLength <- matrix(data = c(11906049, 231977105, 86185990, 2411050, 151410255,
199269234, 34587196, 60357381, 96145497, 620234,
179688604, 66855, 35355928, 134792443, 142986004,
15254573, 6675768, 138039242, 38416654, 96961637), ncol=1)
colnames(normalLength) <- c("length")
### Tests CNpreprocessing() results
context("CNpreprocessing() results")
test_that("CNpreprocessing() must return expected results 01", {
set.seed(444)
results <- CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424, -0.0073122998, 0.0281455711)
expected$segmad <- c(0.0640420795, 0.0476423308, 0.0883320200, 0.0410240773, 0.0752964600)
expected$mediandev <- c(0.022990639976770, 0.009558262267556,
0.013261330082376, -0.070946412101973,
-0.035488541192200)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(1, 1, 1, 1, 1)
expected$marginalprob <- c(0.000000000000000, 0.000000000000000,
0.000139724182812, 0.000000000000000,
0.000000000000000)
expected$maxz <- rep(1, 5)
expected$maxzmean <- c(0.000000000000000, 0.000000000000000,
0.000000000000000, 0.000000000000000,
0.000000000000000)
expected$maxzsigma <- c(0.045757298969319, 0.045757298969319,
0.045757298969319, 0.045757298969319,
0.045757298969319)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(0.992841083588778, 0.991391357872609,
0.992841083588778, 0.000000000000000,
0.000372936761926)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results 02", {
set.seed(424)
results <- CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
"start", "end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=3, minJoin=0.25, cWeight=0.4, bsTimes=1,
chromRange=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424,
-0.0073122998, 0.0281455711)
expected$segmad <- c(0.064042079488653, 0.047642330818085,
0.088332019979936, 0.041024077319856,
0.075296460018356)
expected$mediandev <- c(0.064866978684928, 0.051434600975714,
0.055137668790534, -0.029070073393815,
0.006387797515958)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(1, 0, 0, 1, 0)
expected$marginalprob <- c(0.109372964234594, 0.000000000000000,
0.000000000000000, 0.008601807590315,
0.000000000000000)
expected$maxz <- c(1.000000000000000, 1.000000000000000,
0.538541655965071, 1.000000000000000,
0.990162113892837)
expected$maxzmean <- c(0.000000000000000, 0.059475806154862,
0.048267482678576, 0.000000000000000,
0.048267482678576)
expected$maxzsigma <- c(0.016795531137887, 0.002310603657899,
0.002310603657899, 0.016795531137887,
0.002310603657899)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(1.000000000000000, 1.000000000000000,
1.000000000000000, 0.000372936761926,
0.830608091605016)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results 03", {
set.seed(2211)
results <- CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=3, minJoin=0.25, cWeight=0.2, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424, -0.0073122998, 0.0281455711)
expected$segmad <- c(0.0640420795, 0.0476423308, 0.0883320200, 0.0410240773, 0.0752964600)
expected$mediandev <- c(0.071985431920620, 0.058553054211406, 0.062256122026225, -0.021951620158124, 0.013506250751650)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(0.000000000000, 0.000000000000, 0.000000000000, 1.000000000000000, 0.000000000000)
expected$marginalprob <- c(0.000000000000000, 0.000000000000000, 0.000000000000000, 0.017203615180631, 0.000000000000000)
expected$maxz <- c(1.000000000000000, 1.000000000000000, 0.538541655965071, 1.0000000000000, 0.990162113892837)
expected$maxzmean <- c(0.029023619841193, 0.073987616075458, 0.062779292599172, 0.000000000000000, 0.062779292599172)
expected$maxzsigma <- c(0.002310603657899, 0.002310603657899, 0.002310603657899, 0.011732671852590, 0.002310603657899)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(1.000000000000000, 1.000000000000000, 1.000000000000000, 0.000372936761926, 0.992841083588778)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results when columns names are not the one by default", {
set.seed(2211)
segExampleTmp <- segExample
colnames(segExampleTmp) <- c("Id", "Start", "End", "Num.Probes",
"Seg.Median", "Chrom", "Chrom.Pos.Start",
"Chrom.Pos.End", "Cytoband.Start",
"Cytoband.End", "Abs.Pos.Start", "Abs.Pos.End")
results <- CNpreprocessing(segall=segExampleTmp, ratall=rateExample, idCol="Id",
"Start", "End", chromCol="Chrom", bpStartCol="Chrom.Pos.Start",
bpEndCol="Chrom.Pos.End",
blsize=3, minJoin=0.55, cWeight=0.2, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
colnames(expected)[1:12] <- c("Id", "Start", "End", "Num.Probes",
"Seg.Median", "Chrom", "Chrom.Pos.Start",
"Chrom.Pos.End", "Cytoband.Start",
"Cytoband.End", "Abs.Pos.Start", "Abs.Pos.End")
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424, -0.0073122998, 0.0281455711)
expected$segmad <- c(0.0640420795, 0.0476423308, 0.0883320200, 0.0410240773, 0.0752964600)
expected$mediandev <- c(0.071985431920620, 0.058553054211406, 0.062256122026225, -0.021951620158124, 0.013506250751650)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(0.0000000000000, 0.0000000000000, 0.0000000000000, 1.0000000000000, 0.0000000000000)
expected$marginalprob <- c(0.000000000000, 0.000000000000, 0.000000000000, 0.017203615180631, 0.000000000000)
expected$maxz <- c(1.000000000000, 1.000000000000, 0.538541655965071, 1.000000000000000, 0.990162113892837)
expected$maxzmean <- c(0.029023619841193, 0.073987616075458, 0.062779292599172, 0.000000000000000, 0.062779292599172)
expected$maxzsigma <- c(0.002310603657899, 0.002310603657899, 0.002310603657899, 0.011732671852590, 0.002310603657899)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(1.000000000000, 1.000000000000, 1.000000000000, 0.000372936761926, 0.992841083588778)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results when not ratall", {
results <- CNpreprocessing(segall=segExample, ratall=NULL, "ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
expected <- segExample
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected message when not ratall", {
message <- "No raw table, proceeding to comparison"
expect_output(CNpreprocessing(segall=segExample, ratall=NULL, "ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return error when not idcol", {
message <- "Found unmatched segmented profile IDs"
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol=NULL,
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected message when not idcol and no ratall", {
message <- "Found a single segmented profile with no ID \\nNo raw table, proceeding to comparison"
expect_output(CNpreprocessing(segall=segExample, ratall=NULL, idCol=NULL,
"start", "end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1,
chromRange=1, nJobs=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected results when not idcol and no ratall", {
results <- CNpreprocessing(segall=segExample, ratall=NULL, idCol=NULL,
"start", "end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4,
bsTimes=1, chromRange=1, nJobs=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs)
expected <- segExample
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected error when not startCol and no bpStartCol", {
message <- "Unable to proceed: incomplete segment annotation"
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
startCol=NULL, endCol="end", chromCol="chrom", bpStartCol=NULL,
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when annotation table given without start and chrom column names", {
message <- paste0("No start and chrom column names provided for annotation table\n")
annotationTmp <- data.frame(PROBEID=c(paste0("ZZ-", 1:10)), CHROM=c(rep(1, 10)), CHROM.POS=c(932544, 1036579, 1212746,
1750583, 1750999, 1760583,
1850583, 100394039, 101394030,
106394039))
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
startCol=NULL, endCol=NULL, chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end", annot = annotationTmp,
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=NULL, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when annotation table given without end column name and useEnd set to TRUE", {
message <- paste0("End column name required but not provided in annotation table\n")
annotationTmp <- data.frame(PROBEID=c(paste0("ZZ-", 1:10)), CHROM=c(rep(1, 10)), CHROM.POS=c(932544, 1036579, 1212746,
1750583, 1750999, 1760583,
1850583, 100394039, 101394030,
106394039))
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID", useEnd=TRUE,
startCol=NULL, endCol=NULL, chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end", annot = annotationTmp, annotChromCol="CHROM",
annotStartCol="CHROM.POS",annotEndCol=NULL,
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=NULL, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when annotation table given without end column name and useEnd set to FALSE", {
message <- paste0("Incomplete start and end annotation of segments")
annotationTmp <- data.frame(PROBEID=c(paste0("ZZ-", 1:10)), CHROM=c(rep(1, 10)), CHROM.POS=c(932544, 1036579, 1212746,
1750583, 1750999, 1760583,
1850583, 100394039, 101394030,
106394039))
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID", useEnd=FALSE,
startCol=NULL, endCol=NULL, chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end", annot = annotationTmp, annotChromCol = "CHROM",
annotStartCol="CHROM.POS",annotEndCol=NULL,
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=NULL, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when not startCol and no annotation table", {
message <- "No annotation table; unable to determine boundary probes/bin"
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
startCol=NULL, endCol="end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1,
chromRange=1, nJobs=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when not idcol and ratall with more than 1 numerical column", {
message <- paste0("Ambiguity: more than 1 numeric column in ",
"\"ratall\" matrix. The \"idCol\" ",
"parameter should be specified.\n")
rateExampleTmp <- matrix(data = rep(c(0.0720738404241163, 0.119913919265996, 0.154459489283567, 0.0409946196196852, -0.0828437318817242,
0.0930527245776551, 0.170908929806745, 0.100289489712059, 0.08662475225992, -0.00385501101587094, -0.195791648504205,
0.0636341122831496, 0.109449474459845, 0.043428961427158, 0.160174528536138, 0.0410580626539806, 0.0405224616647681,
0.0986143513758616, 0.0731923745507058, 0.0121261797978406, 0.107795728119586, 0.0832422912347904, 0.0727354592601023,
0.1475937155592, 0.0810554254709479, 0.162564668451733, 0.0590673628590426, -0.0728672744452223, 0.0284354530744622,
0.160126815673499, 0.190799021333644, -0.0269711432208357, 0.0203580612494725, -0.00731229981882388, -0.0440263312613861,
-0.0817496261303279, 0.0146393203392997, 0.0860431917828892, 0.0213604328945665, 0.0789323375946298, 0.0757082196458755,
-0.0507940506094144, 0.0217577735749916, 0.0281455710909498, 0.0196702655955798, 0.154422985605817, 0.260452283950961, 0.122065762785514,
-0.0197506768456278, -0.0277870900508885), 2), ncol = 2)
expect_error(CNpreprocessing(segall=segExample, ratall=rateExampleTmp, idCol=NULL,
startCol=NULL, endCol="end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
KrasnitzLab/CNprep documentation built on May 28, 2022, 8:32 p.m.
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### Unit tests for CNVMetricsMethods.R functions
library(CNprep)
segExample <- data.frame(ID=c(rep("WZ1", 5)),
start=c(1, 16, 23, 31, 38),
end=c(15, 22, 30, 37, 50),
num.probes=c(15, 7, 8, 720, 518),
seg.median=c(0.047797239, -0.215466818, 0.043107477, -0.225908644,
0.037204403),
chrom=c(rep(1, 5)),
chrom.pos.start=c(932544, 16004440, 38093655, 78729960, 103416416),
chrom.pos.end=c(15844870, 37974708, 78619856, 103394039, 142176090),
cytoband.start=c("p36.33", "p36.13", "p34.3", "p31.1", "p21.1"),
cytoband.end=c("p36.13", "p34.3", "p31.1", "p21.1", "q21.1"),
abs.pos.start=c(932544, 16004440, 38093655, 78729960, 103416416),
abs.pos.end=c(15844870, 37974708, 78619856, 103394039, 142176090))
rateExample <- matrix(data = c(0.0720738404241163, 0.119913919265996, 0.154459489283567, 0.0409946196196852, -0.0828437318817242,
0.0930527245776551, 0.170908929806745, 0.100289489712059, 0.08662475225992, -0.00385501101587094, -0.195791648504205,
0.0636341122831496, 0.109449474459845, 0.043428961427158, 0.160174528536138, 0.0410580626539806, 0.0405224616647681,
0.0986143513758616, 0.0731923745507058, 0.0121261797978406, 0.107795728119586, 0.0832422912347904, 0.0727354592601023,
0.1475937155592, 0.0810554254709479, 0.162564668451733, 0.0590673628590426, -0.0728672744452223, 0.0284354530744622,
0.160126815673499, 0.190799021333644, -0.0269711432208357, 0.0203580612494725, -0.00731229981882388, -0.0440263312613861,
-0.0817496261303279, 0.0146393203392997, 0.0860431917828892, 0.0213604328945665, 0.0789323375946298, 0.0757082196458755,
-0.0507940506094144, 0.0217577735749916, 0.0281455710909498, 0.0196702655955798, 0.154422985605817, 0.260452283950961, 0.122065762785514,
-0.0197506768456278, -0.0277870900508885), ncol = 1)
colnames(rateExample) <- c("WZ1")
normSegs <- matrix(data = c(0.023032697, 0.0069878681, 0.0013329618, 0.0110395179,
0.0007606011, 0.0023178528, -0.0076653454, -0.0044130592,
-0.0044268312, -0.0362319897,
0.0001533229, 0.0075387269, 0.0078903700, 0.0007193940,
0.0011609480, 0.0001808010, -0.0172001485, -0.0034588337,
-0.0064778796, -0.0001113585), ncol = 1)
colnames(normSegs) <- c("segmedian")
normalLength <- matrix(data = c(11906049, 231977105, 86185990, 2411050, 151410255,
199269234, 34587196, 60357381, 96145497, 620234,
179688604, 66855, 35355928, 134792443, 142986004,
15254573, 6675768, 138039242, 38416654, 96961637), ncol=1)
colnames(normalLength) <- c("length")
### Tests CNpreprocessing() results
context("CNpreprocessing() results")
test_that("CNpreprocessing() must return expected results 01", {
set.seed(444)
results <- CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424, -0.0073122998, 0.0281455711)
expected$segmad <- c(0.0640420795, 0.0476423308, 0.0883320200, 0.0410240773, 0.0752964600)
expected$mediandev <- c(0.022990639976770, 0.009558262267556,
0.013261330082376, -0.070946412101973,
-0.035488541192200)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(1, 1, 1, 1, 1)
expected$marginalprob <- c(0.000000000000000, 0.000000000000000,
0.000139724182812, 0.000000000000000,
0.000000000000000)
expected$maxz <- rep(1, 5)
expected$maxzmean <- c(0.000000000000000, 0.000000000000000,
0.000000000000000, 0.000000000000000,
0.000000000000000)
expected$maxzsigma <- c(0.045757298969319, 0.045757298969319,
0.045757298969319, 0.045757298969319,
0.045757298969319)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(0.992841083588778, 0.991391357872609,
0.992841083588778, 0.000000000000000,
0.000372936761926)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results 02", {
set.seed(424)
results <- CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
"start", "end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=3, minJoin=0.25, cWeight=0.4, bsTimes=1,
chromRange=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424,
-0.0073122998, 0.0281455711)
expected$segmad <- c(0.064042079488653, 0.047642330818085,
0.088332019979936, 0.041024077319856,
0.075296460018356)
expected$mediandev <- c(0.064866978684928, 0.051434600975714,
0.055137668790534, -0.029070073393815,
0.006387797515958)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(1, 0, 0, 1, 0)
expected$marginalprob <- c(0.109372964234594, 0.000000000000000,
0.000000000000000, 0.008601807590315,
0.000000000000000)
expected$maxz <- c(1.000000000000000, 1.000000000000000,
0.538541655965071, 1.000000000000000,
0.990162113892837)
expected$maxzmean <- c(0.000000000000000, 0.059475806154862,
0.048267482678576, 0.000000000000000,
0.048267482678576)
expected$maxzsigma <- c(0.016795531137887, 0.002310603657899,
0.002310603657899, 0.016795531137887,
0.002310603657899)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(1.000000000000000, 1.000000000000000,
1.000000000000000, 0.000372936761926,
0.830608091605016)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results 03", {
set.seed(2211)
results <- CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=3, minJoin=0.25, cWeight=0.2, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424, -0.0073122998, 0.0281455711)
expected$segmad <- c(0.0640420795, 0.0476423308, 0.0883320200, 0.0410240773, 0.0752964600)
expected$mediandev <- c(0.071985431920620, 0.058553054211406, 0.062256122026225, -0.021951620158124, 0.013506250751650)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(0.000000000000, 0.000000000000, 0.000000000000, 1.000000000000000, 0.000000000000)
expected$marginalprob <- c(0.000000000000000, 0.000000000000000, 0.000000000000000, 0.017203615180631, 0.000000000000000)
expected$maxz <- c(1.000000000000000, 1.000000000000000, 0.538541655965071, 1.0000000000000, 0.990162113892837)
expected$maxzmean <- c(0.029023619841193, 0.073987616075458, 0.062779292599172, 0.000000000000000, 0.062779292599172)
expected$maxzsigma <- c(0.002310603657899, 0.002310603657899, 0.002310603657899, 0.011732671852590, 0.002310603657899)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(1.000000000000000, 1.000000000000000, 1.000000000000000, 0.000372936761926, 0.992841083588778)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results when columns names are not the one by default", {
set.seed(2211)
segExampleTmp <- segExample
colnames(segExampleTmp) <- c("Id", "Start", "End", "Num.Probes",
"Seg.Median", "Chrom", "Chrom.Pos.Start",
"Chrom.Pos.End", "Cytoband.Start",
"Cytoband.End", "Abs.Pos.Start", "Abs.Pos.End")
results <- CNpreprocessing(segall=segExampleTmp, ratall=rateExample, idCol="Id",
"Start", "End", chromCol="Chrom", bpStartCol="Chrom.Pos.Start",
bpEndCol="Chrom.Pos.End",
blsize=3, minJoin=0.55, cWeight=0.2, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
row.names(results) <- NULL
expected <- segExample
colnames(expected)[1:12] <- c("Id", "Start", "End", "Num.Probes",
"Seg.Median", "Chrom", "Chrom.Pos.Start",
"Chrom.Pos.End", "Cytoband.Start",
"Cytoband.End", "Abs.Pos.Start", "Abs.Pos.End")
expected$segmedian <- c(0.0866247523, 0.0731923746, 0.0768954424, -0.0073122998, 0.0281455711)
expected$segmad <- c(0.0640420795, 0.0476423308, 0.0883320200, 0.0410240773, 0.0752964600)
expected$mediandev <- c(0.071985431920620, 0.058553054211406, 0.062256122026225, -0.021951620158124, 0.013506250751650)
expected$segerr <- as.double(rep(NA, 5))
expected$centerz <- c(0.0000000000000, 0.0000000000000, 0.0000000000000, 1.0000000000000, 0.0000000000000)
expected$marginalprob <- c(0.000000000000, 0.000000000000, 0.000000000000, 0.017203615180631, 0.000000000000)
expected$maxz <- c(1.000000000000, 1.000000000000, 0.538541655965071, 1.000000000000000, 0.990162113892837)
expected$maxzmean <- c(0.029023619841193, 0.073987616075458, 0.062779292599172, 0.000000000000000, 0.062779292599172)
expected$maxzsigma <- c(0.002310603657899, 0.002310603657899, 0.002310603657899, 0.011732671852590, 0.002310603657899)
expected$samplesize <- c(111, 75, 41, 67, 42)
expected$negtail <- c(1.000000000000, 1.000000000000, 1.000000000000, 0.000372936761926, 0.992841083588778)
row.names(expected) <- NULL
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected results when not ratall", {
results <- CNpreprocessing(segall=segExample, ratall=NULL, "ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs)
expected <- segExample
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected message when not ratall", {
message <- "No raw table, proceeding to comparison"
expect_output(CNpreprocessing(segall=segExample, ratall=NULL, "ID",
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return error when not idcol", {
message <- "Found unmatched segmented profile IDs"
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol=NULL,
"start", "end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected message when not idcol and no ratall", {
message <- "Found a single segmented profile with no ID \\nNo raw table, proceeding to comparison"
expect_output(CNpreprocessing(segall=segExample, ratall=NULL, idCol=NULL,
"start", "end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1,
chromRange=1, nJobs=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected results when not idcol and no ratall", {
results <- CNpreprocessing(segall=segExample, ratall=NULL, idCol=NULL,
"start", "end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4,
bsTimes=1, chromRange=1, nJobs=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs)
expected <- segExample
expect_equal(results, expected)
})
test_that("CNpreprocessing() must return expected error when not startCol and no bpStartCol", {
message <- "Unable to proceed: incomplete segment annotation"
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
startCol=NULL, endCol="end", chromCol="chrom", bpStartCol=NULL,
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when annotation table given without start and chrom column names", {
message <- paste0("No start and chrom column names provided for annotation table\n")
annotationTmp <- data.frame(PROBEID=c(paste0("ZZ-", 1:10)), CHROM=c(rep(1, 10)), CHROM.POS=c(932544, 1036579, 1212746,
1750583, 1750999, 1760583,
1850583, 100394039, 101394030,
106394039))
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
startCol=NULL, endCol=NULL, chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end", annot = annotationTmp,
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=NULL, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when annotation table given without end column name and useEnd set to TRUE", {
message <- paste0("End column name required but not provided in annotation table\n")
annotationTmp <- data.frame(PROBEID=c(paste0("ZZ-", 1:10)), CHROM=c(rep(1, 10)), CHROM.POS=c(932544, 1036579, 1212746,
1750583, 1750999, 1760583,
1850583, 100394039, 101394030,
106394039))
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID", useEnd=TRUE,
startCol=NULL, endCol=NULL, chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end", annot = annotationTmp, annotChromCol="CHROM",
annotStartCol="CHROM.POS",annotEndCol=NULL,
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=NULL, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when annotation table given without end column name and useEnd set to FALSE", {
message <- paste0("Incomplete start and end annotation of segments")
annotationTmp <- data.frame(PROBEID=c(paste0("ZZ-", 1:10)), CHROM=c(rep(1, 10)), CHROM.POS=c(932544, 1036579, 1212746,
1750583, 1750999, 1760583,
1850583, 100394039, 101394030,
106394039))
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID", useEnd=FALSE,
startCol=NULL, endCol=NULL, chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end", annot = annotationTmp, annotChromCol = "CHROM",
annotStartCol="CHROM.POS",annotEndCol=NULL,
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=NULL, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when not startCol and no annotation table", {
message <- "No annotation table; unable to determine boundary probes/bin"
expect_error(CNpreprocessing(segall=segExample, ratall=rateExample, idCol="ID",
startCol=NULL, endCol="end", chromCol="chrom",
bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1,
chromRange=1, nJobs=1, modelNames="E",
normalLength=normalLength,
normalMedian=normSegs), message)
})
test_that("CNpreprocessing() must return expected error when not idcol and ratall with more than 1 numerical column", {
message <- paste0("Ambiguity: more than 1 numeric column in ",
"\"ratall\" matrix. The \"idCol\" ",
"parameter should be specified.\n")
rateExampleTmp <- matrix(data = rep(c(0.0720738404241163, 0.119913919265996, 0.154459489283567, 0.0409946196196852, -0.0828437318817242,
0.0930527245776551, 0.170908929806745, 0.100289489712059, 0.08662475225992, -0.00385501101587094, -0.195791648504205,
0.0636341122831496, 0.109449474459845, 0.043428961427158, 0.160174528536138, 0.0410580626539806, 0.0405224616647681,
0.0986143513758616, 0.0731923745507058, 0.0121261797978406, 0.107795728119586, 0.0832422912347904, 0.0727354592601023,
0.1475937155592, 0.0810554254709479, 0.162564668451733, 0.0590673628590426, -0.0728672744452223, 0.0284354530744622,
0.160126815673499, 0.190799021333644, -0.0269711432208357, 0.0203580612494725, -0.00731229981882388, -0.0440263312613861,
-0.0817496261303279, 0.0146393203392997, 0.0860431917828892, 0.0213604328945665, 0.0789323375946298, 0.0757082196458755,
-0.0507940506094144, 0.0217577735749916, 0.0281455710909498, 0.0196702655955798, 0.154422985605817, 0.260452283950961, 0.122065762785514,
-0.0197506768456278, -0.0277870900508885), 2), ncol = 2)
expect_error(CNpreprocessing(segall=segExample, ratall=rateExampleTmp, idCol=NULL,
startCol=NULL, endCol="end", chromCol="chrom", bpStartCol="chrom.pos.start",
bpEndCol="chrom.pos.end",
blsize=5, minJoin=0.25, cWeight=0.4, bsTimes=1, chromRange=1, nJobs=1,
modelNames="E", normalLength=normalLength,
normalMedian=normSegs), message)
})
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