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test_that("test_CNE", {
library(GenomicRanges)
CNE12 <- GRangePairs(first=GRanges(seqnames=c("chr13", "chr4", "chr4"),
ranges=IRanges(start=c(71727138,150679343,
146653164),
end=c(71727224, 150679400,
146653221)),
strand="+"),
second=GRanges(seqnames=c("chr1"),
ranges=IRanges(start=c(29854162, 23432387,
35711077),
end=c(29854248, 23432444,
35711134)),
strand="+")
)
CNE21 <- GRangePairs(first=GRanges(seqnames=c("chr1"),
ranges=IRanges(start=c(29854162, 23432387,
35711077),
end=c(29854248, 23432444,
35711134)),
strand="+"),
second=GRanges(seqnames=c("chr13", "chr4", "chr4"),
ranges=IRanges(start=c(71727138,150679343,
146653164),
end=c(71727224, 150679400,
146653221)),
strand="+")
)
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
assembly1Fn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
assembly2Fn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
# Test the validity
## test window < identity
expect_error(CNE(assembly1Fn=assembly1Fn, assembly2Fn=assembly2Fn,
window=49L,
identity=50L, CNE12=CNE12, CNE21=CNE21,
CNEMerged=CNE12, CNEFinal=CNE12, aligner="blat"))
## test number of assembly, aligner >= 2
expect_error(CNE(assembly1Fn=c(assembly1Fn, assembly2Fn),
assembly2Fn=assembly2Fn, window=50L,
identity=50L, CNE12=CNE12, CNE21=CNE21,
CNEMerged=CNE12, CNEFinal=CNE12, aligner="blat"))
expect_error(CNE(assembly1Fn=assembly1Fn,
assembly2Fn=c(assembly1Fn, assembly2Fn), window=50L,
identity=50L, CNE12=CNE12, CNE21=CNE21,
CNEMerged=CNE12, CNEFinal=CNE12, aligner="blat"))
expect_error(CNE(assembly1Fn=assembly1Fn, assembly2Fn=assembly2Fn,
window=50L,
identity=50L, CNE12=CNE12, CNE21=CNE21,
CNEMerged=CNE12, CNEFinal=CNE12, aligner=c("blat", "bwa")))
# Test the getter
cne <- CNE(assembly1Fn=assembly1Fn, assembly2Fn=assembly2Fn,
window=50L, identity=50L,
CNE12=CNE12, CNE21=CNE21, CNEMerged=CNE12, CNEFinal=CNE12,
aligner="blat")
expect_identical(CNE12(cne), CNE12)
expect_identical(CNE21(cne), CNE21)
expect_identical(thresholds(cne), "50_50")
expect_identical(CNEMerged(cne), CNE12)
expect_identical(CNEFinal(cne), CNE12)
}
)
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