inst/unitTests/test_rjmcmcMethod.R
In ArnaudDroitLab/RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
###################################################
# Created by Astrid Deschenes
# 2015-06-30
###################################################
###################################################
## Test the rjmcmcMethod.R functions
###################################################
### {{{ --- Test setup ---
if(FALSE) {
library( "RUnit" )
library( "RJMCMCNucleosomes" )
library( "GenomicRanges")
}
### }}}
data(reads_demo_01)
data(reads_demo_02)
data(RJMCMC_result)
data(syntheticNucleosomeReads)
DIRECTORY <- system.file("extdata", package = "RJMCMCNucleosomes")
file_001 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
pattern = "RJMCMC_seg_01.RDS",
full.names = TRUE)
file_002 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
pattern = "RJMCMC_seg_02.RDS",
full.names = TRUE)
file_003 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
pattern = "RJMCMC_seg_03.RDS",
full.names = TRUE)
###########################################################
## RJMCMC() function
###########################################################
test.rjmcmc_one_read_forward_and_one_read_reverse <- function() {
reads <- GRanges(seqnames = Rle(c("chr1"), c(2)),
ranges = IRanges(101:102, end = 111:112,
names = head(letters, 2)),
strand = Rle(strand(c("-", "+")), c(1, 1)))
obs <- rjmcmc(reads = reads, nbrIterations = 210, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 10,
vSeed = 2211)
exp.k <- 1
exp.k_max <- 1
exp.mu <- c(102)
exp.strand <- c('*')
exp.seqnames <- c("chr1")
message <- paste0(" test.rjmcmc_one_read_forward_and_one_read_reverse() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_01 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 100, lambda = 2, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 1001)
exp.k <- 2
exp.k_max <- 2
exp.mu <- as.integer(c(10080, 10146))
exp.strand <- c('*', '*')
exp.seqnames <- rep("chr_SYNTHETIC", 2)
message <- paste0(" rjmcmc_good_result_01() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_02 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 200, lambda = 3, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 201)
exp.k <- 1
exp.k_max <- 3
exp.mu <- c(10056)
exp.strand <- c('*')
exp.seqnames <- c("chr_SYNTHETIC")
message <- paste0(" rjmcmc_good_result_02() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_03 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 110, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 335,
vSeed = 2011)
exp.k <- 2
exp.k_max <- 4
exp.mu <- c(10058, 10453)
exp.strand <- c('*', '*')
exp.seqnames <- rep("chr_SYNTHETIC", 2)
message <- paste0(" rjmcmc_good_result_03() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_04 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 210, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 10,
vSeed = 2211)
exp.k <- 1
exp.k_max <- 2
exp.mu <- c(10077)
exp.strand <- c('*')
exp.seqnames <- c("chr_SYNTHETIC")
message <- paste0(" test.rjmcmc_good_result_04() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_with_GRanges_with_multiple_names <- function() {
reads <- GRanges(seqnames = Rle(c("chr1", "chr2"), c(5, 5)),
ranges = IRanges(start=c(11:15, 1106:1110), end = c(21:25, 1116:1120),
names = head(letters, 10)),
strand = Rle(strand(c("-", "+", "-", "+", "-")), c(2, 2, 2, 2, 2)))
obs <- rjmcmc(reads = reads, seqName = "chr2",
nbrIterations = 210, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 10,
vSeed = 2211)
exp.k <- 1
exp.k_max <- 1
exp.mu <- c(1107)
exp.strand <- c('*')
exp.seqnames <- c("chr2")
message <- paste0(" test.rjmcmc_good_result_with_GRanges_with_multiple_names() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(as.vector(strand(obs$mu)), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
###########################################################
## mergeAllRDSFilesFromDirectory() function
###########################################################
test.mergeAllRDSFilesFromDirectory_notExisting <- function() {
dir_01 <- "/toto1/toto2/toto3/toto4/toto5/"
dir_02 <- "/toto5/toto4/toto3/toto2/toto1/"
dir <- NULL
if (!file.exists(dir_01)) {
dir <- dir_01
} else {
if (!file.exists(dir_02)) {
dir <- dir_02
}
}
if (!is.null(dir)) {
obs <- tryCatch(mergeAllRDSFilesFromDirectory(dir),
error=conditionMessage)
exp <- paste0("The directory \'", dir,
"\' does not exist.")
message <- paste0(" test.mergeResultFilesInDirectory_notExisting() ",
"- A not existing directory did not generated ",
"expected message.")
checkEquals(obs, exp, msg = message)
}
}
test.mergeAllRDSFilesFromDirectory_good <- function() {
obs <- mergeAllRDSFilesFromDirectory(DIRECTORY)
exp <- list()
exp$k <- 11
listMu <- c(10077, 10236,
10406, 10571,
10744, 10842,
10846, 10896,
10906, 11410,
11580)
exp$mu <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
class(exp) <- "rjmcmcNucleosomesMerge"
message <- paste0(" test.mergeAllRDSFilesFromDirectory_good() ",
"- The mergeAllRDSFilesFromDirectory() did not generated ",
"expected output.")
checkEquals(obs, exp, msg = message)
}
###########################################################
## mergeRDSFiles() function
###########################################################
test.mergeRDSFiles_notExisting <- function() {
file_01 <- "/toto1/toto2/toto3/toto4/toto5/improbable_file_01335320111.RDS"
file_02 <- "/toto5/toto4/toto3/toto2/toto1/improbable_file_01335320111.RDS"
fileName <- array(dim = c(0))
if (!file.exists(file_01)) {
fileName <- c(file_01)
}
if (!file.exists(file_02)) {
fileName <- c(fileName, file_02)
}
if (length(fileName) > 0) {
obs <- tryCatch(mergeRDSFiles(fileName),
error=conditionMessage)
exp <- paste0("The file \'", fileName[1],
"\' does not exist.")
message <- paste0(" test.mergeRDSFiles_notExisting() ",
"- A not existing file did not generated ",
"expected message.")
checkEquals(obs, exp, msg = message)
}
}
test.mergeRDSFiles_good <- function() {
files <- c(file_001, file_002, file_003)
obs <- mergeRDSFiles(files)
exp <- list()
exp$k <- 11
listMu <- c(10077, 10236,
10406, 10571,
10744, 10842,
10846, 10896,
10906, 11410,
11580)
exp$mu <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
class(exp) <- "rjmcmcNucleosomesMerge"
message <- paste0(" test.mergeRDSFiles_good() ",
"- The mergeRDSFiles() did not generated ",
"expected output.")
checkEquals(obs, exp, msg = message)
}
###########################################################
## postTreatment() function
###########################################################
test.postTreatment_good_01 <- function() {
obs <- postTreatment(reads = reads_demo_02,
resultRJMCMC = RJMCMC_result,
extendingSize = 20,
chrLength = 80000)
listMu <- c(10072, 10241,
10574,10665,
10744)
exp <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
message <- paste0(" test.postTreatment_good_01() ",
"- posTreatment() did not generated expected result.")
checkEquals(obs, exp, msg = message)
}
test.postTreatment_good_02 <- function() {
reads <- reads_demo_02
seqlevels(reads)<- c(seqlevels(reads), "chr2")
seqnames(reads)[301:450]<-Rle(values = "chr2", lengths = c(150))
obs <- postTreatment(reads = reads, seqName = "chr_SYNTHETIC",
resultRJMCMC = RJMCMC_result,
extendingSize = 20,
chrLength = 80000)
listMu <- c(10072, 10241, 10574, 10744)
exp <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
message <- paste0(" test.postTreatment_good_02() ",
"- posTreatment() did not generated expected result.")
checkEquals(obs, exp, msg = message)
}
###########################################################
## segmentation() function
###########################################################
test.segmentation_good_01 <- function() {
sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr,
ranges = IRanges(
start = syntheticNucleosomeReads$dataIP$start,
end = syntheticNucleosomeReads$dataIP$end),
strand = syntheticNucleosomeReads$dataIP$strand)
obs <- segmentation(sampleGRanges, zeta = 147, delta = 20, maxLength = 20000)
message <- paste0(" test.segmentation_good_01() ",
"- segmentation() did not generated expected result.")
exp.len = 3
exp.01.len = 10504
exp.02.len = 11873
exp.03.len = 9686
checkTrue(class(obs)=="GRangesList", ms = message)
checkEquals(length(obs), exp.len, ms = message)
checkEquals(length(obs[[1]]), exp.01.len, ms = message)
checkTrue(is(obs[[1]],"GRanges"), ms = message)
checkEquals(length(obs[[2]]), exp.02.len, ms = message)
checkTrue(is(obs[[2]],"GRanges"), ms = message)
checkEquals(length(obs[[3]]), exp.03.len, ms = message)
checkTrue(is(obs[[3]],"GRanges"), ms = message)
}
test.segmentation_good_02 <- function() {
sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr,
ranges = IRanges(
start = syntheticNucleosomeReads$dataIP$start,
end = syntheticNucleosomeReads$dataIP$end),
strand = syntheticNucleosomeReads$dataIP$strand)
obs <- segmentation(sampleGRanges, zeta = 142, delta = 40,
maxLength = 15000)
message <- paste0(" test.segmentation_good_02() ",
"- segmentation() did not generated expected result.")
exp.len = 4
exp.01.len = 7972
exp.02.len = 8572
exp.03.len = 9362
exp.04.len = 6390
checkTrue(class(obs)=="GRangesList", ms = message)
checkEquals(length(obs), exp.len, ms = message)
checkEquals(length(obs[[1]]), exp.01.len, ms = message)
checkTrue(is(obs[[1]],"GRanges"), ms = message)
checkEquals(length(obs[[2]]), exp.02.len, ms = message)
checkTrue(is(obs[[2]],"GRanges"), ms = message)
checkEquals(length(obs[[3]]), exp.03.len, ms = message)
checkTrue(is(obs[[3]],"GRanges"), ms = message)
}
###########################################################
## rjmcmcCHR() function
###########################################################
test.rjmcmcCHR_good_01 <- function() {
temp_dir <- "test_rjmcmcCHR_good_01"
tryCatch({
reads <- GRanges(syntheticNucleosomeReads$dataIP[1:500,])
obs <- rjmcmcCHR(reads = reads,
zeta = 147, delta = 50, maxLength = 1200,
dirOut = temp_dir,
nbrIterations = 1000, lambda = 3, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 10113, nbCores = 2, saveAsRDS = FALSE)
message <- paste0(" test.rjmcmcCHR_good_01() ",
"- rjmcmcCHR() did not generated expected result.")
exp.k <- 2
exp.kPost <- 1
exp.mu <- c(1082, 1193)
exp.muPost <- c(1188)
exp.muStrand <- c('*', '*')
exp.muPost <- c(1188)
exp.muPostStrand <- c('*')
checkTrue(is.list(obs), ms = message)
checkEquals(obs$k, exp.k, ms = message)
checkEquals(obs$kPost, exp.kPost, ms = message)
checkEquals(start(obs$mu), exp.mu, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$mu), exp.mu, ms = message)
checkEquals(as.vector(strand(obs$mu)), exp.muStrand, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$muPost), exp.muPost, ms = message)
checkEquals(as.vector(strand(obs$muPost)), exp.muPostStrand, ms = message)
}, finally = {
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
)
## Double check
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
test.rjmcmcCHR_good_02 <- function() {
temp_dir <- "test_rjmcmcCHR_good_02"
tryCatch({
reads <- GRanges(syntheticNucleosomeReads$dataIP[1:500,])
seqlevels(reads)<- c(seqlevels(reads), "chr2")
seqnames(reads)[400:500]<-Rle(values = "chr2", lengths = c(101))
obs <- rjmcmcCHR(reads = reads, seqName = "chr_SYNTHETIC",
zeta = 147, delta = 50, maxLength = 1200,
dirOut = temp_dir,
nbrIterations = 1000, lambda = 3, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 10113, nbCores = 2, saveAsRDS = FALSE)
message <- paste0(" test.rjmcmcCHR_good_02() ",
"- rjmcmcCHR() did not generated expected result.")
exp.k <- 2
exp.kPost <- 2
exp.mu <- c(1075, 1250)
exp.muPost <- c(1075, 1250)
exp.muStrand <- c('*', '*')
exp.muPost <- c(1075, 1250)
exp.muPostStrand <- c('*', '*')
checkTrue(is.list(obs), ms = message)
checkEquals(obs$k, exp.k, ms = message)
checkEquals(obs$kPost, exp.kPost, ms = message)
checkEquals(start(obs$mu), exp.mu, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$mu), exp.mu, ms = message)
checkEquals(as.vector(strand(obs$mu)), exp.muStrand, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$muPost), exp.muPost, ms = message)
checkEquals(as.vector(strand(obs$muPost)), exp.muPostStrand, ms = message)
}, finally = {
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
)
## Double check
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
ArnaudDroitLab/RJMCMCNucleosomes documentation built on May 5, 2019, 7:06 a.m.
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###################################################
# Created by Astrid Deschenes
# 2015-06-30
###################################################
###################################################
## Test the rjmcmcMethod.R functions
###################################################
### {{{ --- Test setup ---
if(FALSE) {
library( "RUnit" )
library( "RJMCMCNucleosomes" )
library( "GenomicRanges")
}
### }}}
data(reads_demo_01)
data(reads_demo_02)
data(RJMCMC_result)
data(syntheticNucleosomeReads)
DIRECTORY <- system.file("extdata", package = "RJMCMCNucleosomes")
file_001 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
pattern = "RJMCMC_seg_01.RDS",
full.names = TRUE)
file_002 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
pattern = "RJMCMC_seg_02.RDS",
full.names = TRUE)
file_003 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
pattern = "RJMCMC_seg_03.RDS",
full.names = TRUE)
###########################################################
## RJMCMC() function
###########################################################
test.rjmcmc_one_read_forward_and_one_read_reverse <- function() {
reads <- GRanges(seqnames = Rle(c("chr1"), c(2)),
ranges = IRanges(101:102, end = 111:112,
names = head(letters, 2)),
strand = Rle(strand(c("-", "+")), c(1, 1)))
obs <- rjmcmc(reads = reads, nbrIterations = 210, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 10,
vSeed = 2211)
exp.k <- 1
exp.k_max <- 1
exp.mu <- c(102)
exp.strand <- c('*')
exp.seqnames <- c("chr1")
message <- paste0(" test.rjmcmc_one_read_forward_and_one_read_reverse() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_01 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 100, lambda = 2, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 1001)
exp.k <- 2
exp.k_max <- 2
exp.mu <- as.integer(c(10080, 10146))
exp.strand <- c('*', '*')
exp.seqnames <- rep("chr_SYNTHETIC", 2)
message <- paste0(" rjmcmc_good_result_01() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_02 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 200, lambda = 3, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 201)
exp.k <- 1
exp.k_max <- 3
exp.mu <- c(10056)
exp.strand <- c('*')
exp.seqnames <- c("chr_SYNTHETIC")
message <- paste0(" rjmcmc_good_result_02() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_03 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 110, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 335,
vSeed = 2011)
exp.k <- 2
exp.k_max <- 4
exp.mu <- c(10058, 10453)
exp.strand <- c('*', '*')
exp.seqnames <- rep("chr_SYNTHETIC", 2)
message <- paste0(" rjmcmc_good_result_03() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_04 <- function() {
obs <- rjmcmc(reads = reads_demo_01,
nbrIterations = 210, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 10,
vSeed = 2211)
exp.k <- 1
exp.k_max <- 2
exp.mu <- c(10077)
exp.strand <- c('*')
exp.seqnames <- c("chr_SYNTHETIC")
message <- paste0(" test.rjmcmc_good_result_04() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(strand(obs$mu), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
test.rjmcmc_good_result_with_GRanges_with_multiple_names <- function() {
reads <- GRanges(seqnames = Rle(c("chr1", "chr2"), c(5, 5)),
ranges = IRanges(start=c(11:15, 1106:1110), end = c(21:25, 1116:1120),
names = head(letters, 10)),
strand = Rle(strand(c("-", "+", "-", "+", "-")), c(2, 2, 2, 2, 2)))
obs <- rjmcmc(reads = reads, seqName = "chr2",
nbrIterations = 210, lambda = 3, kMax = 30,
minInterval = 100, maxInterval = 200, minReads = 10,
vSeed = 2211)
exp.k <- 1
exp.k_max <- 1
exp.mu <- c(1107)
exp.strand <- c('*')
exp.seqnames <- c("chr2")
message <- paste0(" test.rjmcmc_good_result_with_GRanges_with_multiple_names() ",
"- RJMCMC did not generated expected values")
checkEqualsNumeric(obs$k, exp.k, msg = message)
checkEqualsNumeric(obs$k_max, exp.k_max, msg = message)
checkTrue(class(obs$mu) == "GRanges", msg = message)
checkEqualsNumeric(start(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(end(obs$mu), exp.mu, msg = message)
checkEqualsNumeric(as.vector(strand(obs$mu)), exp.strand, msg = message)
checkEqualsNumeric(seqnames(obs$mu), exp.seqnames, msg = message)
}
###########################################################
## mergeAllRDSFilesFromDirectory() function
###########################################################
test.mergeAllRDSFilesFromDirectory_notExisting <- function() {
dir_01 <- "/toto1/toto2/toto3/toto4/toto5/"
dir_02 <- "/toto5/toto4/toto3/toto2/toto1/"
dir <- NULL
if (!file.exists(dir_01)) {
dir <- dir_01
} else {
if (!file.exists(dir_02)) {
dir <- dir_02
}
}
if (!is.null(dir)) {
obs <- tryCatch(mergeAllRDSFilesFromDirectory(dir),
error=conditionMessage)
exp <- paste0("The directory \'", dir,
"\' does not exist.")
message <- paste0(" test.mergeResultFilesInDirectory_notExisting() ",
"- A not existing directory did not generated ",
"expected message.")
checkEquals(obs, exp, msg = message)
}
}
test.mergeAllRDSFilesFromDirectory_good <- function() {
obs <- mergeAllRDSFilesFromDirectory(DIRECTORY)
exp <- list()
exp$k <- 11
listMu <- c(10077, 10236,
10406, 10571,
10744, 10842,
10846, 10896,
10906, 11410,
11580)
exp$mu <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
class(exp) <- "rjmcmcNucleosomesMerge"
message <- paste0(" test.mergeAllRDSFilesFromDirectory_good() ",
"- The mergeAllRDSFilesFromDirectory() did not generated ",
"expected output.")
checkEquals(obs, exp, msg = message)
}
###########################################################
## mergeRDSFiles() function
###########################################################
test.mergeRDSFiles_notExisting <- function() {
file_01 <- "/toto1/toto2/toto3/toto4/toto5/improbable_file_01335320111.RDS"
file_02 <- "/toto5/toto4/toto3/toto2/toto1/improbable_file_01335320111.RDS"
fileName <- array(dim = c(0))
if (!file.exists(file_01)) {
fileName <- c(file_01)
}
if (!file.exists(file_02)) {
fileName <- c(fileName, file_02)
}
if (length(fileName) > 0) {
obs <- tryCatch(mergeRDSFiles(fileName),
error=conditionMessage)
exp <- paste0("The file \'", fileName[1],
"\' does not exist.")
message <- paste0(" test.mergeRDSFiles_notExisting() ",
"- A not existing file did not generated ",
"expected message.")
checkEquals(obs, exp, msg = message)
}
}
test.mergeRDSFiles_good <- function() {
files <- c(file_001, file_002, file_003)
obs <- mergeRDSFiles(files)
exp <- list()
exp$k <- 11
listMu <- c(10077, 10236,
10406, 10571,
10744, 10842,
10846, 10896,
10906, 11410,
11580)
exp$mu <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
class(exp) <- "rjmcmcNucleosomesMerge"
message <- paste0(" test.mergeRDSFiles_good() ",
"- The mergeRDSFiles() did not generated ",
"expected output.")
checkEquals(obs, exp, msg = message)
}
###########################################################
## postTreatment() function
###########################################################
test.postTreatment_good_01 <- function() {
obs <- postTreatment(reads = reads_demo_02,
resultRJMCMC = RJMCMC_result,
extendingSize = 20,
chrLength = 80000)
listMu <- c(10072, 10241,
10574,10665,
10744)
exp <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
message <- paste0(" test.postTreatment_good_01() ",
"- posTreatment() did not generated expected result.")
checkEquals(obs, exp, msg = message)
}
test.postTreatment_good_02 <- function() {
reads <- reads_demo_02
seqlevels(reads)<- c(seqlevels(reads), "chr2")
seqnames(reads)[301:450]<-Rle(values = "chr2", lengths = c(150))
obs <- postTreatment(reads = reads, seqName = "chr_SYNTHETIC",
resultRJMCMC = RJMCMC_result,
extendingSize = 20,
chrLength = 80000)
listMu <- c(10072, 10241, 10574, 10744)
exp <- GRanges(seqnames = rep("chr_SYNTHETIC",length(listMu)),
ranges=IRanges(start=listMu,end=listMu),
strand=rep("*", length(listMu)))
message <- paste0(" test.postTreatment_good_02() ",
"- posTreatment() did not generated expected result.")
checkEquals(obs, exp, msg = message)
}
###########################################################
## segmentation() function
###########################################################
test.segmentation_good_01 <- function() {
sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr,
ranges = IRanges(
start = syntheticNucleosomeReads$dataIP$start,
end = syntheticNucleosomeReads$dataIP$end),
strand = syntheticNucleosomeReads$dataIP$strand)
obs <- segmentation(sampleGRanges, zeta = 147, delta = 20, maxLength = 20000)
message <- paste0(" test.segmentation_good_01() ",
"- segmentation() did not generated expected result.")
exp.len = 3
exp.01.len = 10504
exp.02.len = 11873
exp.03.len = 9686
checkTrue(class(obs)=="GRangesList", ms = message)
checkEquals(length(obs), exp.len, ms = message)
checkEquals(length(obs[[1]]), exp.01.len, ms = message)
checkTrue(is(obs[[1]],"GRanges"), ms = message)
checkEquals(length(obs[[2]]), exp.02.len, ms = message)
checkTrue(is(obs[[2]],"GRanges"), ms = message)
checkEquals(length(obs[[3]]), exp.03.len, ms = message)
checkTrue(is(obs[[3]],"GRanges"), ms = message)
}
test.segmentation_good_02 <- function() {
sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr,
ranges = IRanges(
start = syntheticNucleosomeReads$dataIP$start,
end = syntheticNucleosomeReads$dataIP$end),
strand = syntheticNucleosomeReads$dataIP$strand)
obs <- segmentation(sampleGRanges, zeta = 142, delta = 40,
maxLength = 15000)
message <- paste0(" test.segmentation_good_02() ",
"- segmentation() did not generated expected result.")
exp.len = 4
exp.01.len = 7972
exp.02.len = 8572
exp.03.len = 9362
exp.04.len = 6390
checkTrue(class(obs)=="GRangesList", ms = message)
checkEquals(length(obs), exp.len, ms = message)
checkEquals(length(obs[[1]]), exp.01.len, ms = message)
checkTrue(is(obs[[1]],"GRanges"), ms = message)
checkEquals(length(obs[[2]]), exp.02.len, ms = message)
checkTrue(is(obs[[2]],"GRanges"), ms = message)
checkEquals(length(obs[[3]]), exp.03.len, ms = message)
checkTrue(is(obs[[3]],"GRanges"), ms = message)
}
###########################################################
## rjmcmcCHR() function
###########################################################
test.rjmcmcCHR_good_01 <- function() {
temp_dir <- "test_rjmcmcCHR_good_01"
tryCatch({
reads <- GRanges(syntheticNucleosomeReads$dataIP[1:500,])
obs <- rjmcmcCHR(reads = reads,
zeta = 147, delta = 50, maxLength = 1200,
dirOut = temp_dir,
nbrIterations = 1000, lambda = 3, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 10113, nbCores = 2, saveAsRDS = FALSE)
message <- paste0(" test.rjmcmcCHR_good_01() ",
"- rjmcmcCHR() did not generated expected result.")
exp.k <- 2
exp.kPost <- 1
exp.mu <- c(1082, 1193)
exp.muPost <- c(1188)
exp.muStrand <- c('*', '*')
exp.muPost <- c(1188)
exp.muPostStrand <- c('*')
checkTrue(is.list(obs), ms = message)
checkEquals(obs$k, exp.k, ms = message)
checkEquals(obs$kPost, exp.kPost, ms = message)
checkEquals(start(obs$mu), exp.mu, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$mu), exp.mu, ms = message)
checkEquals(as.vector(strand(obs$mu)), exp.muStrand, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$muPost), exp.muPost, ms = message)
checkEquals(as.vector(strand(obs$muPost)), exp.muPostStrand, ms = message)
}, finally = {
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
)
## Double check
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
test.rjmcmcCHR_good_02 <- function() {
temp_dir <- "test_rjmcmcCHR_good_02"
tryCatch({
reads <- GRanges(syntheticNucleosomeReads$dataIP[1:500,])
seqlevels(reads)<- c(seqlevels(reads), "chr2")
seqnames(reads)[400:500]<-Rle(values = "chr2", lengths = c(101))
obs <- rjmcmcCHR(reads = reads, seqName = "chr_SYNTHETIC",
zeta = 147, delta = 50, maxLength = 1200,
dirOut = temp_dir,
nbrIterations = 1000, lambda = 3, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
vSeed = 10113, nbCores = 2, saveAsRDS = FALSE)
message <- paste0(" test.rjmcmcCHR_good_02() ",
"- rjmcmcCHR() did not generated expected result.")
exp.k <- 2
exp.kPost <- 2
exp.mu <- c(1075, 1250)
exp.muPost <- c(1075, 1250)
exp.muStrand <- c('*', '*')
exp.muPost <- c(1075, 1250)
exp.muPostStrand <- c('*', '*')
checkTrue(is.list(obs), ms = message)
checkEquals(obs$k, exp.k, ms = message)
checkEquals(obs$kPost, exp.kPost, ms = message)
checkEquals(start(obs$mu), exp.mu, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$mu), exp.mu, ms = message)
checkEquals(as.vector(strand(obs$mu)), exp.muStrand, ms = message)
checkEquals(start(obs$muPost), exp.muPost, ms = message)
checkEquals(end(obs$muPost), exp.muPost, ms = message)
checkEquals(as.vector(strand(obs$muPost)), exp.muPostStrand, ms = message)
}, finally = {
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
)
## Double check
if (dir.exists(temp_dir)) {
unlink(temp_dir, recursive = TRUE, force = FALSE)
}
}
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