tests/testthat/test-breakIntoCNPs.chrom.R
In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events
### Unit tests for breakIntoCNPs.chrom.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 breakIntoCNPs.chrom() results
context("breakIntoCNPs.chrom() results")
test_that("breakIntoCNPs.chrom() must return expected results 01", {
segTableTemp01 <- 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(0.037797239, -0.515466818, 0.143107477, -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),
eventIndex=c(0,0,1,0,-1))
cnptableTemp01 <- matrix(c(rep(1, 3), c(932544, 38093688, 123416446),
c(11844870, 48619856, 182176090), rep(1,3)), ncol=4, byrow=FALSE)
colnames(cnptableTemp01) <- c("chrom", "start", "end", "cnpindex")
RNGkind("default")
set.seed(111223)
results <- CNprep:::breakIntoCNPs.chrom(segTable=segTableTemp01, chrom="chrom",
startPos="chrom.pos.start", endPos="chrom.pos.end",
startProbe="start",
endProbe="end",
eventIndex="eventIndex",
cnpTable=cnptableTemp01, cnpChrom="chrom",
cnpStart="start", cnpEnd="end", cnpIndex="cnpindex",
minCover=0.005, indexVals=c(-1, 1))
expected <- matrix(c(1, 16, 23, 25, 38, 15, 24, 30, 37, 50, 0, 0, 1, 0, 0), ncol=3, byrow=FALSE)
colnames(expected) <- c("start", "end", "toremove")
expect_equal(results, expected)
})
test_that("breakIntoCNPs.chrom() must return expected results when eventIndex all zero", {
segTableTemp01 <- 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(0.037797239, -0.515466818, 0.143107477, -0.225908644,
0.037204403),
chrom=c(rep(2, 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),
eventIndex=c(0,0,0,0,0))
cnptableTemp01 <- matrix(c(rep(1, 3), c(932544, 38093688, 123416446),
c(11844870, 48619856, 182176090), rep(1,3)), ncol=4, byrow=FALSE)
colnames(cnptableTemp01) <- c("chrom", "start", "end", "cnpindex")
RNGkind("default")
set.seed(123)
results <- CNprep:::breakIntoCNPs.chrom(segTable=segTableTemp01, chrom="chrom",
startPos="chrom.pos.start", endPos="chrom.pos.end",
startProbe="start",
endProbe="end",
eventIndex="eventIndex",
cnpTable=cnptableTemp01, cnpChrom="chrom",
cnpStart="start", cnpEnd="end", cnpIndex="cnpindex",
minCover=0.005, indexVals=c(-1, 1))
expected <- matrix(c(1, 16, 23, 31, 38, 15, 22, 30, 37, 50, 0, 0, 0, 0, 0), ncol=3, byrow=FALSE)
colnames(expected) <- c("start", "end", "toremove")
expect_equal(results, expected)
})
test_that("breakIntoCNPs.chrom() must return expected results 02", {
segTableTemp01 <- 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(0.037797239, -0.515466818, 0.143107477, -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),
eventIndex=c(0,0,1,1,0))
cnptableTemp01 <- matrix(c(rep(1, 3), c(932544, 38093688, 123416446),
c(11844870, 58619856, 182176090), rep(1,3)), ncol=4, byrow=FALSE)
colnames(cnptableTemp01) <- c("chrom", "start", "end", "cnpindex")
RNGkind("default")
set.seed(111)
results <- CNprep:::breakIntoCNPs.chrom(segTable=segTableTemp01, chrom="chrom",
startPos="chrom.pos.start", endPos="chrom.pos.end",
startProbe="start",
endProbe="end",
eventIndex="eventIndex",
cnpTable=cnptableTemp01, cnpChrom="chrom",
cnpStart="start", cnpEnd="end", cnpIndex="cnpindex",
minCover=0.005, indexVals=c(-1, 1))
expected <- matrix(c(1, 16, 23, 26, 38, 15, 25, 30, 37, 50, 0, 0, 1, 0, 0), ncol=3, byrow=FALSE)
colnames(expected) <- c("start", "end", "toremove")
expect_equal(results, expected)
})
KrasnitzLab/CNprep documentation built on May 28, 2022, 8:32 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.
### Unit tests for breakIntoCNPs.chrom.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 breakIntoCNPs.chrom() results
context("breakIntoCNPs.chrom() results")
test_that("breakIntoCNPs.chrom() must return expected results 01", {
segTableTemp01 <- 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(0.037797239, -0.515466818, 0.143107477, -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),
eventIndex=c(0,0,1,0,-1))
cnptableTemp01 <- matrix(c(rep(1, 3), c(932544, 38093688, 123416446),
c(11844870, 48619856, 182176090), rep(1,3)), ncol=4, byrow=FALSE)
colnames(cnptableTemp01) <- c("chrom", "start", "end", "cnpindex")
RNGkind("default")
set.seed(111223)
results <- CNprep:::breakIntoCNPs.chrom(segTable=segTableTemp01, chrom="chrom",
startPos="chrom.pos.start", endPos="chrom.pos.end",
startProbe="start",
endProbe="end",
eventIndex="eventIndex",
cnpTable=cnptableTemp01, cnpChrom="chrom",
cnpStart="start", cnpEnd="end", cnpIndex="cnpindex",
minCover=0.005, indexVals=c(-1, 1))
expected <- matrix(c(1, 16, 23, 25, 38, 15, 24, 30, 37, 50, 0, 0, 1, 0, 0), ncol=3, byrow=FALSE)
colnames(expected) <- c("start", "end", "toremove")
expect_equal(results, expected)
})
test_that("breakIntoCNPs.chrom() must return expected results when eventIndex all zero", {
segTableTemp01 <- 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(0.037797239, -0.515466818, 0.143107477, -0.225908644,
0.037204403),
chrom=c(rep(2, 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),
eventIndex=c(0,0,0,0,0))
cnptableTemp01 <- matrix(c(rep(1, 3), c(932544, 38093688, 123416446),
c(11844870, 48619856, 182176090), rep(1,3)), ncol=4, byrow=FALSE)
colnames(cnptableTemp01) <- c("chrom", "start", "end", "cnpindex")
RNGkind("default")
set.seed(123)
results <- CNprep:::breakIntoCNPs.chrom(segTable=segTableTemp01, chrom="chrom",
startPos="chrom.pos.start", endPos="chrom.pos.end",
startProbe="start",
endProbe="end",
eventIndex="eventIndex",
cnpTable=cnptableTemp01, cnpChrom="chrom",
cnpStart="start", cnpEnd="end", cnpIndex="cnpindex",
minCover=0.005, indexVals=c(-1, 1))
expected <- matrix(c(1, 16, 23, 31, 38, 15, 22, 30, 37, 50, 0, 0, 0, 0, 0), ncol=3, byrow=FALSE)
colnames(expected) <- c("start", "end", "toremove")
expect_equal(results, expected)
})
test_that("breakIntoCNPs.chrom() must return expected results 02", {
segTableTemp01 <- 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(0.037797239, -0.515466818, 0.143107477, -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),
eventIndex=c(0,0,1,1,0))
cnptableTemp01 <- matrix(c(rep(1, 3), c(932544, 38093688, 123416446),
c(11844870, 58619856, 182176090), rep(1,3)), ncol=4, byrow=FALSE)
colnames(cnptableTemp01) <- c("chrom", "start", "end", "cnpindex")
RNGkind("default")
set.seed(111)
results <- CNprep:::breakIntoCNPs.chrom(segTable=segTableTemp01, chrom="chrom",
startPos="chrom.pos.start", endPos="chrom.pos.end",
startProbe="start",
endProbe="end",
eventIndex="eventIndex",
cnpTable=cnptableTemp01, cnpChrom="chrom",
cnpStart="start", cnpEnd="end", cnpIndex="cnpindex",
minCover=0.005, indexVals=c(-1, 1))
expected <- matrix(c(1, 16, 23, 26, 38, 15, 25, 30, 37, 50, 0, 0, 1, 0, 0), ncol=3, byrow=FALSE)
colnames(expected) <- c("start", "end", "toremove")
expect_equal(results, expected)
})
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.