inst/unitTests/test_coordinate-mapping-methods.R
In Bioconductor/GenomicFeatures: Conveniently import and query gene models
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
cdsbytx <- cdsBy(txdb, "tx", use.names=TRUE)[1:3]
quiet <- suppressWarnings
### ----------------------------------------------------------------------
### mapFromTranscripts(), pmapFromTranscripts()
test_mapFromTranscripts <- function()
{
## empty
ans1 <- mapFromTranscripts(GRanges(), GRanges())
ans2 <- mapFromTranscripts(GRanges(), GRangesList())
checkIdentical(ans1, ans2)
checkIdentical(names(mcols(ans1)), c("xHits", "transcriptsHits"))
## 'transcripts' must have names
x <- GRanges("tx1", IRanges(1, 5), strand="+")
gr <- GRanges("chr1", IRanges(c(1, 20), width=10), strand="+")
checkException(mapFromTranscripts(x, gr), silent=TRUE)
checkException(mapFromTranscripts(x, GRangesList(gr, gr)), silent=TRUE)
}
test_mapFromTranscripts_strand <- function()
{
x <- GRanges("tx1", IRanges(1, 5), strand="+")
gr <- GRanges("chr1", IRanges(c(1, 20), width=10), strand="+")
names(gr) <- c("tx1", "tx1")
align = GRangesList(gr, gr, gr)
names(align) <- c("tx1", "bar", "tx1")
## "+' strand
ans <- mapFromTranscripts(x, align) ## GRangesList
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 3L))
checkIdentical(ranges(ans), IRanges(c(1, 1), c(5, 5)))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, align, TRUE)
checkIdentical(ranges(ans), ranges(ignore))
checkTrue(unique(as.character(strand(ignore))) == "*")
ans <- mapFromTranscripts(x, gr) ## GRanges
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 2L))
checkIdentical(ranges(ans), IRanges(c(1, 20), c(5, 24)))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, gr, TRUE)
checkIdentical(ranges(ans), ranges(ignore))
checkTrue(unique(as.character(strand(ignore))) == "*")
## '-' strand
xx <- GRanges("tx1", IRanges(12, 14), strand="-")
gg <- GRanges("chr1", IRanges(c(1, 20), width=10), strand="-")
aa = GRangesList(gg)
names(aa) <- "tx1"
ans <- mapFromTranscripts(xx, aa)
checkIdentical(ranges(ans), IRanges(7, 9))
## invalid mixed strand
strand(align[[1]][1]) <- "-"
checkException(mapFromTranscripts(x, align, FALSE), silent=TRUE)
## valid mixed strand:
strand(align[[1]]) <- "-"
ans <- mapFromTranscripts(x, align) ## GRangesList
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, 3L)
checkIdentical(ranges(ans), IRanges(1, 5))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, align, TRUE)
checkIdentical(mcols(ignore)$transcriptsHits, c(1L, 3L))
checkTrue(unique(as.character(strand(ignore))) == "*")
strand(x) <- "-"
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(25, end=29))
strand(gr[2]) <- "-"
strand(x) <- "+"
ans <- mapFromTranscripts(x, gr) ## GRanges
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, 1L)
checkIdentical(ranges(ans), IRanges(1, 5))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, gr, TRUE)
checkIdentical(ranges(ignore), IRanges(c(1, 20), c(5, 24)))
checkTrue(unique(as.character(strand(ignore))) == "*")
strand(x) <- "-"
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(25, end=29))
}
test_mapFromTranscripts_order_in_GRangesList <- function()
{
x <- GRanges("tx1", IRanges(1, 5), strand="+")
gr1 <- GRanges("chr1", IRanges(c(1, 20), end=c(10, 30)), strand="+")
gr2 <- GRanges("chr1", IRanges(c(20, 1), end=c(30, 10)), strand="+")
align <- GRangesList(gr1, gr2); names(align) <- c("tx1", "tx1")
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(c(1, 1), c(5, 5)))
checkIdentical(mcols(ans)$xHits, c(1L, 1L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 2L))
strand(x) <- strand(align) <- "-"
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(c(26, 26), c(30, 30)))
checkIdentical(mcols(ans)$xHits, c(1L, 1L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 2L))
}
test_pmapFromTranscripts <- function()
{
## empty
ans1 <- pmapFromTranscripts(IRanges(), GRanges())
ans2 <- pmapFromTranscripts(IRanges(), GRangesList())
ans3 <- pmapFromTranscripts(GRanges(), GRanges())
ans4 <- pmapFromTranscripts(GRanges(), GRangesList())
checkTrue(length(ans1) == length(ans2))
checkTrue(length(ans3) == length(ans4))
checkTrue(length(ans1) == 0L)
checkTrue(is(ans1, "GRanges"))
checkTrue(is(ans2, "GRangesList"))
checkTrue(is(ans3, "GRanges"))
checkTrue(is(ans4, "GRangesList"))
}
test_pmapFromTranscripts_recycling <- function()
{
x <- GRanges("tx1", IRanges(c(1, 1, 1), width=5), strand="+")
gr <- GRanges("chr1", IRanges(c(10, 10, 10), width=10), strand="+")
checkException(pmapFromTranscripts(x[1:2], gr), silent=TRUE)
checkException(pmapFromTranscripts(x, gr[1:2]), silent=TRUE)
## 'transcripts' as GRanges
ans1 <- pmapFromTranscripts(x[1], gr)
ans2 <- pmapFromTranscripts(x, gr[1])
checkIdentical(ans1, ans2)
ans1 <- pmapFromTranscripts(ranges(x[1]), gr)
ans2 <- pmapFromTranscripts(ranges(x), gr[1])
checkIdentical(ans1, ans2)
checkIdentical(names(mcols(ans1)), character(0))
## 'transcripts' as GRangesList
grl <- split(gr, seq_along(gr))
ans1 <- pmapFromTranscripts(x[1], grl)
ans2 <- pmapFromTranscripts(x, grl[1])
checkIdentical(unname(ans1), unname(ans2))
ans1 <- pmapFromTranscripts(ranges(x[1]), grl)
ans2 <- pmapFromTranscripts(ranges(x), grl[1])
checkIdentical(unname(ans1), unname(ans2))
}
test_pmapFromTranscripts_strand <- function()
{
x <- GRanges("chr1", IRanges(1, 5))
align <- GRangesList(
GRanges("chr1", IRanges(c(201, 101), c(220, 120)), strand="-"),
GRanges("chr1", IRanges(501, 535), strand="+"))
ans <- pmapFromTranscripts(ranges(x), align)
checkIdentical(width(ans), IntegerList(c(5, 0), 5))
checkIdentical(start(ans), IntegerList(c(216, 101), 501))
## 'x' is "*"
ans <- pmapFromTranscripts(x, align)
checkIdentical(width(ans), IntegerList(c(5, 0), 5))
checkIdentical(start(ans), IntegerList(c(216, 101), 501))
## 'x' is "+"
strand(x) <- "+"
ans <- pmapFromTranscripts(x, align)
checkIdentical(width(ans), IntegerList(c(0, 0), 5))
checkIdentical(start(ans), IntegerList(c(201, 101), 501))
## 'x' is "-"
strand(x) <- "-"
ans <- pmapFromTranscripts(x, align)
checkIdentical(width(ans), IntegerList(c(5, 0), 0))
checkIdentical(start(ans), IntegerList(c(216, 101), 501))
## ignore.strand
ans <- pmapFromTranscripts(x, align, TRUE)
checkIdentical(width(ans), IntegerList(c(0, 5), 5))
checkIdentical(start(ans), IntegerList(c(201, 101), 501))
checkIdentical(as.character(runValue(strand(ans))), c("*", "*"))
## order of ranges in return GRangesList
strand(align) <- strand(x) <- "+"
ans <- pmapFromTranscripts(x, align)
## invalid mixed strand
x <- GRanges("chr1", IRanges(1, 5), strand="+")
align <- GRangesList(
GRanges("chr1", IRanges(c(1, 1), width=5), strand=c("+", "-")))
checkException(pmapFromTranscripts(x, align), silent=TRUE)
checkException(pmapFromTranscripts(ranges(x), align), silent=TRUE)
}
test_pmapFromTranscripts_UNMAPPED <- function()
{
## 'transcripts' is GRanges
x <- GRanges("chr1", IRanges(40, 50))
align <- GRanges("chr1", IRanges(35, width=5))
ans <- pmapFromTranscripts(x, align, TRUE)
checkIdentical(as.character(seqnames(ans)), "UNMAPPED")
checkTrue(width(ans) == 0L)
}
### ----------------------------------------------------------------------
### mapToTranscripts(), pmapToTranscripts()
test_mapToTranscripts <- function()
{
## empty
ans1 <- mapToTranscripts(GRanges(), GRanges())
ans2 <- mapToTranscripts(GRanges(), GRangesList())
checkTrue(length(ans1) == 0L)
checkTrue(length(ans2) == 0L)
checkIdentical(names(mcols(ans1)), c("xHits", "transcriptsHits"))
checkIdentical(names(mcols(ans2)), c("xHits", "transcriptsHits"))
## strand
x <- GRanges("chr2L", IRanges(c(7500, 8400, 9000),
width=200, names=LETTERS[1:3]), strand="+")
align <- cdsbytx
ans <- mapToTranscripts(x, cdsbytx, ignore.strand=FALSE)
checkTrue(length(ans) == 3L)
checkIdentical(names(ans), c("B", "B", "C"))
checkTrue(all(width(ans) == 200L))
checkIdentical(mcols(ans)$xHits, c(2L, 2L, 3L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 3L, 2L))
strand(align[[2]][1]) <- "-"
checkException(mapToTranscripts(x, align, FALSE, FALSE), silent=TRUE)
strand(align[[2]]) <- "-"
ans <- mapToTranscripts(x, align, ignore.strand=FALSE)
checkIdentical(mcols(ans)$xHits, c(2L, 2L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 3L))
checkIdentical(names(ans), c("B", "B"))
checkIdentical(seqlengths(ans), sum(width(align)))
x <- GRanges("chr3", IRanges(9, 9), strand="+")
transcripts <- GRangesList(tx1=GRanges("chr3", IRanges(3, 10), strand="-"))
ans <- mapToTranscripts(x, transcripts)
checkTrue(length(ans) == 0L)
ans <- mapToTranscripts(x, transcripts, TRUE)
checkTrue(start(ans) == 7L)
checkTrue(as.character(strand(ans)) == "*")
x <- GRanges("1", IRanges(248, width=1))
transcripts <- GRangesList(
foo = (GRanges("1", IRanges(c(101,201), width=50), strand="-")))
ans <- mapToTranscripts(x, transcripts, TRUE)
checkIdentical(ranges(ans), IRanges(98, 98))
checkTrue(as.character(strand(ans)) == "*")
ans <- mapToTranscripts(x, transcripts, FALSE)
checkIdentical(ranges(ans), IRanges(3, 3))
checkTrue(as.character(strand(ans)) == "-")
## TxDb
x <- GRanges("chr2L", IRanges(c(7500, 8400, 9000),
width=200, names=LETTERS[1:3]))
checkException(mapToTranscripts(x, txdb, extractor.fun="foo"), silent=TRUE)
ans <- mapToTranscripts(x, txdb, extractor.fun=exonsBy, by="tx")
checkIdentical(names(ans), c("B", "B", rep("C", 3)))
checkIdentical(as.character(seqnames(ans)), as.character(c(1, 3, 1, 2, 3)))
ans <- mapToTranscripts(x, txdb, extractor.fun=exonsBy, by="gene")
checkIdentical(mcols(ans)$transcriptsHits, rep(4179L, 5))
checkIdentical(seqlengths(ans), sum(width(exonsBy(txdb, by="gene"))))
}
test_mapToTranscripts_range_order <- function()
{
x <- GRanges("chrA", IRanges(43522349, width=1), strand="+")
align1 <- GRangesList(GRanges("chrA",
IRanges(c(43522244, 43528406),
c(43524145, 43528644)), strand="+"))
align2 <- GRangesList(GRanges("chrA",
IRanges(c(43528406, 43522244),
c(43528644, 43524145)), strand="+"))
names(align1) <- names(align2) <- LETTERS[seq_along(align1)]
## "+" strand
## smallest range first
ans <- mapToTranscripts(x, align1, FALSE)
checkTrue(start(ans) == 106L)
## largest range first
ans <- mapToTranscripts(x, align2, FALSE)
checkTrue(start(ans) == 106L)
## "-" strand
strand(x) <- "-"
strand(align1) <- "-"
strand(align2) <- "-"
## smallest range first
ans <- mapToTranscripts(x, align1, FALSE)
checkTrue(start(ans) == 2036L)
## largest range first
ans <- mapToTranscripts(x, align2, FALSE)
checkTrue(start(ans) == 2036L)
}
test_mapToTranscripts_span_introns <- function()
{
x <- GRanges("chr1", IRanges(start=c(11, 11, 21, 11, 40),
end=c(12, 23, 33, 33, 45)), strand="-")
align <- GRangesList(GRanges("chr1",
IRanges(start=c(10, 20, 30), width=5), strand = "-"))
names(align) <- LETTERS[seq_along(align)]
ans <- mapToTranscripts(x, align)
target <- IRanges(c(13, 7, 2, 2), c(14, 14, 9, 14))
checkIdentical(ranges(ans), target)
}
test_pmapToTranscripts <- function()
{
## empty
ans1 <- pmapToTranscripts(GRanges(), GRanges())
ans2 <- pmapToTranscripts(GRanges(), GRangesList())
checkTrue(length(ans1) == 0L)
checkTrue(length(ans2) == 0L)
checkIdentical(names(mcols(ans1)), character(0))
checkIdentical(names(mcols(ans2)), character(0))
## methods GR,GR GR,GRL
## recycling
x <- GRanges("chr1", IRanges(1, width=1))
y <- GRanges("chr1", IRanges(1:5, width=1))
ans <- pmapToTranscripts(x, GRangesList("tx1"=y, "tx2"=y))
checkIdentical(as.character(seqnames(ans)), c("tx1", "tx2"))
ans <- pmapToTranscripts(c(x, x), GRangesList("tx1"=y))
checkIdentical(as.character(seqnames(ans)), c("tx1", "tx1"))
## strand
x <- GRanges("chr1", IRanges(c(6, 16, 1), width=1, names=LETTERS[1:3]))
align <- GRangesList(GRanges("chr1", IRanges(5, 10)),
GRanges("chr1", IRanges(c(5, 15), width=6)),
GRanges("chr1", IRanges(5, 10)))
names(align) <- letters[seq_along(align)]
strand(x) <- "-"
strand(align) <- "+"
ans <- pmapToTranscripts(x, align, FALSE)
checkTrue(length(x) == length(x))
checkTrue(all(width(ans) == 0L))
checkIdentical(names(ans), LETTERS[seq_along(align)])
strand(align[[2]][1]) <- "-"
checkException(pmapToTranscripts(x, align, FALSE), silent=TRUE)
strand(align) <- "+"
strand(x) <- "+"
ans <- pmapToTranscripts(x, align, FALSE)
checkIdentical(width(ans), c(1L, 1L, 0L))
checkIdentical(start(ans), c(2L, 8L, 0L))
strand(align) <- "-"
strand(x) <- "-"
ans <- pmapToTranscripts(x, align, FALSE)
checkIdentical(width(ans), c(1L, 1L, 0L))
checkIdentical(start(ans), c(5L, 5L, 0L))
checkIdentical(names(ans), names(x))
checkIdentical(seqlevels(ans), c("a", "b", "c"))
checkIdentical(as.character(strand(ans)), c("-", "-", "*"))
## out of bounds
x <- GRanges("chr1", IRanges(rep(40, 4), width=11))
align <- GRanges("chr1", IRanges(c(1, 35, 45, 55), width=11))
ans <- pmapToTranscripts(x, align)
checkIdentical(seqnames(ans), Rle(as.factor(1:4)))
}
test_mapToTranscripts_intronJunctions <- function()
{
## 2 out of bounds, intron, true hit
x <- GRanges("chr1", IRanges(start=c(1, 6, 8, 15), width=1))
align <- GRangesList(
"A"=GRanges("chr1", IRanges(start=c(5, 10), end=c(6, 12))))
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(length(ans) == 2)
checkEquals(mcols(ans)$xHits, c(2, 3))
checkEquals(width(ans), c(1, 0))
checkEquals(start(ans), c(2, 3))
checkEquals(mcols(ans)$intronic, c(FALSE, TRUE))
ans <- mapToTranscripts(rev(x), align, intronJunctions=TRUE)
checkEquals(width(ans), c(0, 1))
checkEquals(mcols(ans)$intronic, c(TRUE, FALSE))
## span intron and exon
x <- GRanges("chr1", IRanges(start=6, end=7))
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(length(ans) == 0)
## no non-hits
x <- GRanges("chr1", IRanges(start=5, end=6))
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(ranges(ans) == IRanges(1, 2))
checkEquals(mcols(ans)$intronic, logical(1))
## negative strand
x <- GRanges("chr1", IRanges(start=c(1, 6, 8, 15), width=1))
align <- GRangesList(
"A"=GRanges("chr1", IRanges(start=c(5, 10), end=c(6, 12))))
strand(x) <- strand(align) <- "-"
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(length(ans) == 2)
checkEquals(width(ans), c(1, 0))
checkEquals(start(ans), c(4, 4))
}
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library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
cdsbytx <- cdsBy(txdb, "tx", use.names=TRUE)[1:3]
quiet <- suppressWarnings
### ----------------------------------------------------------------------
### mapFromTranscripts(), pmapFromTranscripts()
test_mapFromTranscripts <- function()
{
## empty
ans1 <- mapFromTranscripts(GRanges(), GRanges())
ans2 <- mapFromTranscripts(GRanges(), GRangesList())
checkIdentical(ans1, ans2)
checkIdentical(names(mcols(ans1)), c("xHits", "transcriptsHits"))
## 'transcripts' must have names
x <- GRanges("tx1", IRanges(1, 5), strand="+")
gr <- GRanges("chr1", IRanges(c(1, 20), width=10), strand="+")
checkException(mapFromTranscripts(x, gr), silent=TRUE)
checkException(mapFromTranscripts(x, GRangesList(gr, gr)), silent=TRUE)
}
test_mapFromTranscripts_strand <- function()
{
x <- GRanges("tx1", IRanges(1, 5), strand="+")
gr <- GRanges("chr1", IRanges(c(1, 20), width=10), strand="+")
names(gr) <- c("tx1", "tx1")
align = GRangesList(gr, gr, gr)
names(align) <- c("tx1", "bar", "tx1")
## "+' strand
ans <- mapFromTranscripts(x, align) ## GRangesList
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 3L))
checkIdentical(ranges(ans), IRanges(c(1, 1), c(5, 5)))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, align, TRUE)
checkIdentical(ranges(ans), ranges(ignore))
checkTrue(unique(as.character(strand(ignore))) == "*")
ans <- mapFromTranscripts(x, gr) ## GRanges
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 2L))
checkIdentical(ranges(ans), IRanges(c(1, 20), c(5, 24)))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, gr, TRUE)
checkIdentical(ranges(ans), ranges(ignore))
checkTrue(unique(as.character(strand(ignore))) == "*")
## '-' strand
xx <- GRanges("tx1", IRanges(12, 14), strand="-")
gg <- GRanges("chr1", IRanges(c(1, 20), width=10), strand="-")
aa = GRangesList(gg)
names(aa) <- "tx1"
ans <- mapFromTranscripts(xx, aa)
checkIdentical(ranges(ans), IRanges(7, 9))
## invalid mixed strand
strand(align[[1]][1]) <- "-"
checkException(mapFromTranscripts(x, align, FALSE), silent=TRUE)
## valid mixed strand:
strand(align[[1]]) <- "-"
ans <- mapFromTranscripts(x, align) ## GRangesList
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, 3L)
checkIdentical(ranges(ans), IRanges(1, 5))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, align, TRUE)
checkIdentical(mcols(ignore)$transcriptsHits, c(1L, 3L))
checkTrue(unique(as.character(strand(ignore))) == "*")
strand(x) <- "-"
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(25, end=29))
strand(gr[2]) <- "-"
strand(x) <- "+"
ans <- mapFromTranscripts(x, gr) ## GRanges
checkTrue(all(width(ans) == 5L))
checkIdentical(mcols(ans)$transcriptsHits, 1L)
checkIdentical(ranges(ans), IRanges(1, 5))
checkIdentical(unique(as.character(seqnames(ans))), "chr1")
ignore <- mapFromTranscripts(x, gr, TRUE)
checkIdentical(ranges(ignore), IRanges(c(1, 20), c(5, 24)))
checkTrue(unique(as.character(strand(ignore))) == "*")
strand(x) <- "-"
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(25, end=29))
}
test_mapFromTranscripts_order_in_GRangesList <- function()
{
x <- GRanges("tx1", IRanges(1, 5), strand="+")
gr1 <- GRanges("chr1", IRanges(c(1, 20), end=c(10, 30)), strand="+")
gr2 <- GRanges("chr1", IRanges(c(20, 1), end=c(30, 10)), strand="+")
align <- GRangesList(gr1, gr2); names(align) <- c("tx1", "tx1")
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(c(1, 1), c(5, 5)))
checkIdentical(mcols(ans)$xHits, c(1L, 1L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 2L))
strand(x) <- strand(align) <- "-"
ans <- mapFromTranscripts(x, align)
checkIdentical(ranges(ans), IRanges(c(26, 26), c(30, 30)))
checkIdentical(mcols(ans)$xHits, c(1L, 1L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 2L))
}
test_pmapFromTranscripts <- function()
{
## empty
ans1 <- pmapFromTranscripts(IRanges(), GRanges())
ans2 <- pmapFromTranscripts(IRanges(), GRangesList())
ans3 <- pmapFromTranscripts(GRanges(), GRanges())
ans4 <- pmapFromTranscripts(GRanges(), GRangesList())
checkTrue(length(ans1) == length(ans2))
checkTrue(length(ans3) == length(ans4))
checkTrue(length(ans1) == 0L)
checkTrue(is(ans1, "GRanges"))
checkTrue(is(ans2, "GRangesList"))
checkTrue(is(ans3, "GRanges"))
checkTrue(is(ans4, "GRangesList"))
}
test_pmapFromTranscripts_recycling <- function()
{
x <- GRanges("tx1", IRanges(c(1, 1, 1), width=5), strand="+")
gr <- GRanges("chr1", IRanges(c(10, 10, 10), width=10), strand="+")
checkException(pmapFromTranscripts(x[1:2], gr), silent=TRUE)
checkException(pmapFromTranscripts(x, gr[1:2]), silent=TRUE)
## 'transcripts' as GRanges
ans1 <- pmapFromTranscripts(x[1], gr)
ans2 <- pmapFromTranscripts(x, gr[1])
checkIdentical(ans1, ans2)
ans1 <- pmapFromTranscripts(ranges(x[1]), gr)
ans2 <- pmapFromTranscripts(ranges(x), gr[1])
checkIdentical(ans1, ans2)
checkIdentical(names(mcols(ans1)), character(0))
## 'transcripts' as GRangesList
grl <- split(gr, seq_along(gr))
ans1 <- pmapFromTranscripts(x[1], grl)
ans2 <- pmapFromTranscripts(x, grl[1])
checkIdentical(unname(ans1), unname(ans2))
ans1 <- pmapFromTranscripts(ranges(x[1]), grl)
ans2 <- pmapFromTranscripts(ranges(x), grl[1])
checkIdentical(unname(ans1), unname(ans2))
}
test_pmapFromTranscripts_strand <- function()
{
x <- GRanges("chr1", IRanges(1, 5))
align <- GRangesList(
GRanges("chr1", IRanges(c(201, 101), c(220, 120)), strand="-"),
GRanges("chr1", IRanges(501, 535), strand="+"))
ans <- pmapFromTranscripts(ranges(x), align)
checkIdentical(width(ans), IntegerList(c(5, 0), 5))
checkIdentical(start(ans), IntegerList(c(216, 101), 501))
## 'x' is "*"
ans <- pmapFromTranscripts(x, align)
checkIdentical(width(ans), IntegerList(c(5, 0), 5))
checkIdentical(start(ans), IntegerList(c(216, 101), 501))
## 'x' is "+"
strand(x) <- "+"
ans <- pmapFromTranscripts(x, align)
checkIdentical(width(ans), IntegerList(c(0, 0), 5))
checkIdentical(start(ans), IntegerList(c(201, 101), 501))
## 'x' is "-"
strand(x) <- "-"
ans <- pmapFromTranscripts(x, align)
checkIdentical(width(ans), IntegerList(c(5, 0), 0))
checkIdentical(start(ans), IntegerList(c(216, 101), 501))
## ignore.strand
ans <- pmapFromTranscripts(x, align, TRUE)
checkIdentical(width(ans), IntegerList(c(0, 5), 5))
checkIdentical(start(ans), IntegerList(c(201, 101), 501))
checkIdentical(as.character(runValue(strand(ans))), c("*", "*"))
## order of ranges in return GRangesList
strand(align) <- strand(x) <- "+"
ans <- pmapFromTranscripts(x, align)
## invalid mixed strand
x <- GRanges("chr1", IRanges(1, 5), strand="+")
align <- GRangesList(
GRanges("chr1", IRanges(c(1, 1), width=5), strand=c("+", "-")))
checkException(pmapFromTranscripts(x, align), silent=TRUE)
checkException(pmapFromTranscripts(ranges(x), align), silent=TRUE)
}
test_pmapFromTranscripts_UNMAPPED <- function()
{
## 'transcripts' is GRanges
x <- GRanges("chr1", IRanges(40, 50))
align <- GRanges("chr1", IRanges(35, width=5))
ans <- pmapFromTranscripts(x, align, TRUE)
checkIdentical(as.character(seqnames(ans)), "UNMAPPED")
checkTrue(width(ans) == 0L)
}
### ----------------------------------------------------------------------
### mapToTranscripts(), pmapToTranscripts()
test_mapToTranscripts <- function()
{
## empty
ans1 <- mapToTranscripts(GRanges(), GRanges())
ans2 <- mapToTranscripts(GRanges(), GRangesList())
checkTrue(length(ans1) == 0L)
checkTrue(length(ans2) == 0L)
checkIdentical(names(mcols(ans1)), c("xHits", "transcriptsHits"))
checkIdentical(names(mcols(ans2)), c("xHits", "transcriptsHits"))
## strand
x <- GRanges("chr2L", IRanges(c(7500, 8400, 9000),
width=200, names=LETTERS[1:3]), strand="+")
align <- cdsbytx
ans <- mapToTranscripts(x, cdsbytx, ignore.strand=FALSE)
checkTrue(length(ans) == 3L)
checkIdentical(names(ans), c("B", "B", "C"))
checkTrue(all(width(ans) == 200L))
checkIdentical(mcols(ans)$xHits, c(2L, 2L, 3L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 3L, 2L))
strand(align[[2]][1]) <- "-"
checkException(mapToTranscripts(x, align, FALSE, FALSE), silent=TRUE)
strand(align[[2]]) <- "-"
ans <- mapToTranscripts(x, align, ignore.strand=FALSE)
checkIdentical(mcols(ans)$xHits, c(2L, 2L))
checkIdentical(mcols(ans)$transcriptsHits, c(1L, 3L))
checkIdentical(names(ans), c("B", "B"))
checkIdentical(seqlengths(ans), sum(width(align)))
x <- GRanges("chr3", IRanges(9, 9), strand="+")
transcripts <- GRangesList(tx1=GRanges("chr3", IRanges(3, 10), strand="-"))
ans <- mapToTranscripts(x, transcripts)
checkTrue(length(ans) == 0L)
ans <- mapToTranscripts(x, transcripts, TRUE)
checkTrue(start(ans) == 7L)
checkTrue(as.character(strand(ans)) == "*")
x <- GRanges("1", IRanges(248, width=1))
transcripts <- GRangesList(
foo = (GRanges("1", IRanges(c(101,201), width=50), strand="-")))
ans <- mapToTranscripts(x, transcripts, TRUE)
checkIdentical(ranges(ans), IRanges(98, 98))
checkTrue(as.character(strand(ans)) == "*")
ans <- mapToTranscripts(x, transcripts, FALSE)
checkIdentical(ranges(ans), IRanges(3, 3))
checkTrue(as.character(strand(ans)) == "-")
## TxDb
x <- GRanges("chr2L", IRanges(c(7500, 8400, 9000),
width=200, names=LETTERS[1:3]))
checkException(mapToTranscripts(x, txdb, extractor.fun="foo"), silent=TRUE)
ans <- mapToTranscripts(x, txdb, extractor.fun=exonsBy, by="tx")
checkIdentical(names(ans), c("B", "B", rep("C", 3)))
checkIdentical(as.character(seqnames(ans)), as.character(c(1, 3, 1, 2, 3)))
ans <- mapToTranscripts(x, txdb, extractor.fun=exonsBy, by="gene")
checkIdentical(mcols(ans)$transcriptsHits, rep(4179L, 5))
checkIdentical(seqlengths(ans), sum(width(exonsBy(txdb, by="gene"))))
}
test_mapToTranscripts_range_order <- function()
{
x <- GRanges("chrA", IRanges(43522349, width=1), strand="+")
align1 <- GRangesList(GRanges("chrA",
IRanges(c(43522244, 43528406),
c(43524145, 43528644)), strand="+"))
align2 <- GRangesList(GRanges("chrA",
IRanges(c(43528406, 43522244),
c(43528644, 43524145)), strand="+"))
names(align1) <- names(align2) <- LETTERS[seq_along(align1)]
## "+" strand
## smallest range first
ans <- mapToTranscripts(x, align1, FALSE)
checkTrue(start(ans) == 106L)
## largest range first
ans <- mapToTranscripts(x, align2, FALSE)
checkTrue(start(ans) == 106L)
## "-" strand
strand(x) <- "-"
strand(align1) <- "-"
strand(align2) <- "-"
## smallest range first
ans <- mapToTranscripts(x, align1, FALSE)
checkTrue(start(ans) == 2036L)
## largest range first
ans <- mapToTranscripts(x, align2, FALSE)
checkTrue(start(ans) == 2036L)
}
test_mapToTranscripts_span_introns <- function()
{
x <- GRanges("chr1", IRanges(start=c(11, 11, 21, 11, 40),
end=c(12, 23, 33, 33, 45)), strand="-")
align <- GRangesList(GRanges("chr1",
IRanges(start=c(10, 20, 30), width=5), strand = "-"))
names(align) <- LETTERS[seq_along(align)]
ans <- mapToTranscripts(x, align)
target <- IRanges(c(13, 7, 2, 2), c(14, 14, 9, 14))
checkIdentical(ranges(ans), target)
}
test_pmapToTranscripts <- function()
{
## empty
ans1 <- pmapToTranscripts(GRanges(), GRanges())
ans2 <- pmapToTranscripts(GRanges(), GRangesList())
checkTrue(length(ans1) == 0L)
checkTrue(length(ans2) == 0L)
checkIdentical(names(mcols(ans1)), character(0))
checkIdentical(names(mcols(ans2)), character(0))
## methods GR,GR GR,GRL
## recycling
x <- GRanges("chr1", IRanges(1, width=1))
y <- GRanges("chr1", IRanges(1:5, width=1))
ans <- pmapToTranscripts(x, GRangesList("tx1"=y, "tx2"=y))
checkIdentical(as.character(seqnames(ans)), c("tx1", "tx2"))
ans <- pmapToTranscripts(c(x, x), GRangesList("tx1"=y))
checkIdentical(as.character(seqnames(ans)), c("tx1", "tx1"))
## strand
x <- GRanges("chr1", IRanges(c(6, 16, 1), width=1, names=LETTERS[1:3]))
align <- GRangesList(GRanges("chr1", IRanges(5, 10)),
GRanges("chr1", IRanges(c(5, 15), width=6)),
GRanges("chr1", IRanges(5, 10)))
names(align) <- letters[seq_along(align)]
strand(x) <- "-"
strand(align) <- "+"
ans <- pmapToTranscripts(x, align, FALSE)
checkTrue(length(x) == length(x))
checkTrue(all(width(ans) == 0L))
checkIdentical(names(ans), LETTERS[seq_along(align)])
strand(align[[2]][1]) <- "-"
checkException(pmapToTranscripts(x, align, FALSE), silent=TRUE)
strand(align) <- "+"
strand(x) <- "+"
ans <- pmapToTranscripts(x, align, FALSE)
checkIdentical(width(ans), c(1L, 1L, 0L))
checkIdentical(start(ans), c(2L, 8L, 0L))
strand(align) <- "-"
strand(x) <- "-"
ans <- pmapToTranscripts(x, align, FALSE)
checkIdentical(width(ans), c(1L, 1L, 0L))
checkIdentical(start(ans), c(5L, 5L, 0L))
checkIdentical(names(ans), names(x))
checkIdentical(seqlevels(ans), c("a", "b", "c"))
checkIdentical(as.character(strand(ans)), c("-", "-", "*"))
## out of bounds
x <- GRanges("chr1", IRanges(rep(40, 4), width=11))
align <- GRanges("chr1", IRanges(c(1, 35, 45, 55), width=11))
ans <- pmapToTranscripts(x, align)
checkIdentical(seqnames(ans), Rle(as.factor(1:4)))
}
test_mapToTranscripts_intronJunctions <- function()
{
## 2 out of bounds, intron, true hit
x <- GRanges("chr1", IRanges(start=c(1, 6, 8, 15), width=1))
align <- GRangesList(
"A"=GRanges("chr1", IRanges(start=c(5, 10), end=c(6, 12))))
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(length(ans) == 2)
checkEquals(mcols(ans)$xHits, c(2, 3))
checkEquals(width(ans), c(1, 0))
checkEquals(start(ans), c(2, 3))
checkEquals(mcols(ans)$intronic, c(FALSE, TRUE))
ans <- mapToTranscripts(rev(x), align, intronJunctions=TRUE)
checkEquals(width(ans), c(0, 1))
checkEquals(mcols(ans)$intronic, c(TRUE, FALSE))
## span intron and exon
x <- GRanges("chr1", IRanges(start=6, end=7))
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(length(ans) == 0)
## no non-hits
x <- GRanges("chr1", IRanges(start=5, end=6))
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(ranges(ans) == IRanges(1, 2))
checkEquals(mcols(ans)$intronic, logical(1))
## negative strand
x <- GRanges("chr1", IRanges(start=c(1, 6, 8, 15), width=1))
align <- GRangesList(
"A"=GRanges("chr1", IRanges(start=c(5, 10), end=c(6, 12))))
strand(x) <- strand(align) <- "-"
ans <- mapToTranscripts(x, align, intronJunctions=TRUE)
checkTrue(length(ans) == 2)
checkEquals(width(ans), c(1, 0))
checkEquals(start(ans), c(4, 4))
}
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