Nothing
setwd(file.path(getwd(), "testdata"))
context("Test that getSeqsFromGRs() function works correctly")
test_that("getSeqsFromGRs() generates the correct data structure", {
gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
# Create the backSplicedJunctions without retriving the missing coordinates
backSplicedJunctions <- getBackSplicedJunctions(gtf)
mergedBSJunctions <-
mergeBSJunctions(backSplicedJunctions, gtf)
# Annonate BSJs
annotatedBSJs <- annotateBSJs(mergedBSJunctions, gtf)
if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
# Get BSgenome object
genome <-
BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
# type = "ie"
targets <-
getSeqsFromGRs(
annotatedBSJs,
genome,
lIntron = 100,
lExon = 9,
type = "ie"
)
expect_is(targets, "list")
expect_equal(
colnames(targets$upGR),
c(
"id",
"gene",
"transcript",
"strand",
"chrom",
"startGR",
"endGR",
"length",
"seq",
"type"
)
)
expect_equal(nrow(targets$upGR), nrow(annotatedBSJs))
# type = "bse"
targets <-
getSeqsFromGRs(
annotatedBSJs,
genome,
lIntron = 100,
lExon = 9,
type = "bse"
)
expect_is(targets, "list")
expect_equal(
colnames(targets$upGR),
c(
"id",
"gene",
"transcript",
"strand",
"chrom",
"startGR",
"endGR",
"length",
"seq",
"type"
)
)
expect_equal(nrow(targets$upGR), nrow(annotatedBSJs))
# type = "fi"
targets <-
getSeqsFromGRs(
annotatedBSJs,
genome,
lIntron = 100,
lExon = 9,
type = "fi"
)
expect_is(targets, "list")
expect_equal(
colnames(targets$upGR),
c(
"id",
"gene",
"transcript",
"strand",
"chrom",
"startGR",
"endGR",
"length",
"seq",
"type"
)
)
expect_equal(nrow(targets$upGR), nrow(annotatedBSJs))
} else{
cat(
"Missing package BSgenome.Mmusculus.UCSC.mm10.
Use BiocManager to install it."
)
}
})
test_that("getSeqFromGRs() retrieves the correct genomic ranges when type = ie",
{
gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
# Create the backSplicedJunctions without retriving the missing coordinates
backSplicedJunctions <- getBackSplicedJunctions(gtf)
mergedBSJunctions <-
mergeBSJunctions(backSplicedJunctions, gtf)
# Annonate BSJs
annotatedBSJs <- annotateBSJs(mergedBSJunctions, gtf)
if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
# Get BSgenome object
genome <-
BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
targets <- getSeqsFromGRs(
annotatedBSJs,
genome,
lIntron = 100,
lExon = 9,
type = "ie"
)
# Check Raph1:-:chr1:60533406:60525592
expect_lt(targets$upGR$startGR[4], targets$upGR$endGR[4])
expect_lt(targets$downGR$startGR[4], targets$downGR$endGR[4])
# Check Creb1:+:chr1:64550849:64576329
expect_lt(targets$upGR$startGR[3], targets$upGR$endGR[3])
expect_lt(targets$downGR$startGR[3], targets$downGR$endGR[3])
# Check
expect_equal(targets$upGR$startGR[4], 60533397)
expect_equal(targets$upGR$endGR[4], 60533506)
expect_equal(targets$downGR$startGR[4], 60525492)
expect_equal(targets$downGR$endGR[4], 60525601)
# Check
expect_equal(targets$upGR$startGR[3], 64550749)
expect_equal(targets$upGR$endGR[3], 64550858)
expect_equal(targets$downGR$startGR[3], 64576320)
expect_equal(targets$downGR$endGR[3], 64576429)
# Check
expect_equal(targets$upGR$startGR[9], 155440776)
expect_equal(targets$upGR$endGR[9], 155440887)
expect_equal(targets$downGR$startGR[9], 155437759)
expect_equal(targets$downGR$endGR[9], 155437869)
# Check
expect_equal(targets$upGR$startGR[11], 52516077)
expect_equal(targets$upGR$endGR[11], 52516086)
expect_equal(targets$downGR$startGR[11], 52542627)
expect_equal(targets$downGR$endGR[11], 52542736)
# Check
expect_equal(targets$upGR$startGR[1], 43704434)
expect_equal(targets$upGR$endGR[1], 43704543)
expect_equal(targets$downGR$startGR[1], 43705468)
expect_equal(targets$downGR$endGR[1], 43705577)
# Check whether the right sequences are retrieved
expect_equal(substr(targets$upGR$seq[4], 1, 20),
"AUUUAACUUCAGAGAGUCAC")
expect_equal(substr(targets$downGR$seq[4], 1, 20),
"AAUUACUGAGGUAAAUAGAG")
expect_equal(substr(targets$upGR$seq[3], 1, 20),
"UUAACCACCACAUAGCCUAU")
expect_equal(substr(targets$downGR$seq[3], 1, 20),
"UGAAGAACAGGUACAGAUUC")
} else{
cat(
"Missing package BSgenome.Mmusculus.UCSC.mm10.
Use BiocManager to install it."
)
}
})
test_that("getSeqsFromGRs() extracts BSJ coordinates when type = bse", {
gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
# Create the backSplicedJunctions without retriving the missing coordinates
backSplicedJunctions <- getBackSplicedJunctions(GTFFile())
mergedBSJunctions <- mergeBSJunctions(backSplicedJunctions, gtf)
# Annonate BSJs
annotatedBSJs <- annotateBSJs(mergedBSJunctions, gtf)
if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
# Get BSgenome object
genome <-
BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
targets <- getSeqsFromGRs(annotatedBSJs,
genome,
type = "bse")
expect_lt(targets$upGR$startGR[4], targets$upGR$endGR[4])
expect_lt(targets$downGR$startGR[4], targets$downGR$endGR[4])
expect_lt(targets$upGR$startGR[3], targets$upGR$endGR[3])
expect_lt(targets$downGR$startGR[3], targets$downGR$endGR[3])
#we know that for the reported row of our test data the strand is negative
expect_equal(targets$upGR$startGR[4], 60533287)
expect_equal(targets$upGR$endGR[4], 60533406)
expect_equal(targets$downGR$startGR[4], 60525592)
expect_equal(targets$downGR$endGR[4], 60526100)
# we know that for the reported row in our test data the strand is positive
expect_equal(targets$upGR$startGR[3], 64550849)
expect_equal(targets$upGR$endGR[3], 64550970)
expect_equal(targets$downGR$startGR[3], 64576179)
expect_equal(targets$downGR$endGR[3], 64576329)
# Check whether the right sequences are retrieved
expect_equal(substr(targets$upGR$seq[4], 1, 20),
"AUGGAGCAACUAUCCGAUGA")
expect_equal(substr(targets$downGR$seq[4], 1, 20),
"AAGCUCUGAAUCAGGGUGAG")
expect_equal(substr(targets$upGR$seq[3], 1, 20),
"GUAACUAAAUGACCAUGGAA")
expect_equal(substr(targets$downGR$seq[3], 1, 20),
"CUGCCUCAGGCGAUGUACAA")
} else{
cat(
"Missing package BSgenome.Mmusculus.UCSC.mm10.
Use BiocManager to install it."
)
}
})
test_that("getSeqsFromGRs() extracts the coordinates of the flanking introns
whhen type = fi",
{
gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
# Create the backSplicedJunctions without retriving the missing coordinates
backSplicedJunctions <- getBackSplicedJunctions(gtf)
mergedBSJunctions <-
mergeBSJunctions(backSplicedJunctions, gtf)
# Annonate BSJs
annotatedBSJs <- annotateBSJs(mergedBSJunctions, gtf)
if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
# Get BSgenome object
genome <-
BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
targets <- getSeqsFromGRs(annotatedBSJs,
genome,
type = "fi")
expect_lt(targets$upGR$startGR[4], targets$upGR$endGR[4])
expect_lt(targets$downGR$startGR[4], targets$downGR$endGR[4])
expect_lt(targets$upGR$startGR[3], targets$upGR$endGR[3])
expect_lt(targets$downGR$startGR[3], targets$downGR$endGR[3])
# we know that for the reported row of our test data the strand is negative
expect_equal(targets$upGR$startGR[4], 60533407)
expect_equal(targets$upGR$endGR[4], 60566564)
expect_equal(targets$downGR$startGR[4], 60503596)
expect_equal(targets$downGR$endGR[4], 60525591)
# we know that for the reported row in our test data the strand is positive
expect_equal(targets$upGR$startGR[3], 64533021)
expect_equal(targets$upGR$endGR[3], 64550848)
expect_equal(targets$downGR$startGR[3], 64576330)
expect_equal(targets$downGR$endGR[3], 64597233)
# Check whether the right sequences are retrieved
expect_equal(substr(targets$upGR$seq[4], 1, 20),
"GUGAGUGCUCCGCCACCUGG")
expect_equal(substr(targets$downGR$seq[4], 1, 20),
"GUAAAUAGAGAAAAUUUCUC")
expect_equal(substr(targets$upGR$seq[3], 1, 20),
"GUAAGAGGAGCAGGAGGAGG")
expect_equal(substr(targets$downGR$seq[3], 1, 20),
"GUACAGAUUCCAAACACUUA")
} else{
cat(
"Missing package BSgenome.Mmusculus.UCSC.mm10.
Use BiocManager to install it."
)
}
})
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