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###
test_transcriptsByOverlaps <- function()
{
txdb <- loadDb(system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures"))
checkException(transcriptsByOverlaps(txdb), silent = TRUE)
checkException(transcriptsByOverlaps(txdb, IRanges()), silent = TRUE)
checkException(transcriptsByOverlaps(txdb, GRanges(), columns = "bad"),
silent = TRUE)
seqinfo <- seqinfo(txdb)
seqlevels <- seqlevels(seqinfo)
gr <- GRanges(seqnames = "chrX",
ranges = IRanges(start=54071000, width=1),
strand = strand("-"))
want <-
GRanges(seqnames = factor("chrX", levels = seqlevels),
ranges = IRanges(start=53963113, end=54071569),
strand = strand("-"),
tx_id = 147L,
tx_name = "uc004dsu.3")
seqinfo(want) <- seqinfo
want <- GenomicFeatures:::.assignMetadataList(want, txdb)
checkIdentical(transcriptsByOverlaps(txdb, gr), want)
ranges <- IRanges(start = c(113000000, 54071000, 54071000),
width = c( 5000000, 1, 1))
chrom <- c("chr3", "chrX", "chrX")
strand <- strand(c("+", "+", "-"))
gr <- GRanges(seqnames = chrom, ranges = ranges, strand = strand)
want <- GRanges(seqnames =
factor(c("chr3", "chr3", "chr3", "chrX"),
levels = seqlevels),
ranges = IRanges(start = c(113666748, 113666822, 113676421,
53963113),
end = c(113681827, 113681827, 113682211,
54071569)),
strand = strand(c("+", "+", "+", "-")),
tx_id = c(29:31, 147L))
seqinfo(want) <- seqinfo
want <- GenomicFeatures:::.assignMetadataList(want, txdb)
checkIdentical(transcriptsByOverlaps(txdb, gr, columns="tx_id"), want)
}
test_exonsByOverlaps <- function()
{
txdb <- loadDb(system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures"))
checkException(exonsByOverlaps(txdb), silent = TRUE)
checkException(exonsByOverlaps(txdb, IRanges()), silent = TRUE)
checkException(exonsByOverlaps(txdb, GRanges(), columns = "bad"),
silent = TRUE)
seqinfo <- seqinfo(txdb)
seqlevels <- seqlevels(seqinfo)
gr <- GRanges(seqnames = "chr3",
ranges = IRanges(start=113677210, width=1),
strand = strand("+"))
want <-
GRanges(seqnames = factor("chr3", levels = seqlevels),
ranges = IRanges(start=c(113677210, 113677210),
end =c(113677385, 113682211)),
strand = strand("+"),
exon_id = 139:140)
seqinfo(want) <- seqinfo
want <- GenomicFeatures:::.assignMetadataList(want, txdb)
checkIdentical(exonsByOverlaps(txdb, gr), want)
}
test_cdsByOverlaps <- function()
{
txdb <- loadDb(system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures"))
checkException(cdsByOverlaps(txdb), silent = TRUE)
checkException(cdsByOverlaps(txdb, IRanges()), silent = TRUE)
checkException(cdsByOverlaps(txdb, GRanges(), columns = "bad"),
silent = TRUE)
seqinfo <- seqinfo(txdb)
seqlevels <- seqlevels(seqinfo)
gr <- GRanges(seqnames = "chr3",
ranges = IRanges(start=113677210, width=1),
strand = strand("+"))
want <-
GRanges(seqnames = factor("chr3", levels = seqlevels),
ranges = IRanges(start=c(113677210, 113677210),
end =c(113677385, 113677477)),
strand = strand("+"),
cds_id = 116:117)
seqinfo(want) <- seqinfo
want <- GenomicFeatures:::.assignMetadataList(want, txdb)
checkIdentical(cdsByOverlaps(txdb, gr), want)
}
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