Assigns region types such as
Only the biotypes that are likely to have a pol II promoter will be
filtered in. This is currently hardcoded in the function; see its source
code. Example of biotypes without a pol II promoter: VDJ segments, miRNA,
but also snoRNA, etc. Thus, the Intergenic category displayed in output of
plotAnnot may include counts overlaping with real exons of discarded
transcribed regions: be careful that large percentages do not necessarly
suggest abundance of novel promoters.
A Run-length-encoded (
Rle) factor of same length as the
object, indicating if the interval is
unknown, or just
unknown if the
metadata is absent.
1 2 3 4 5 6 7 8 9 10 11 12
CAGEr:::ranges2annot(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot) ctss <- GenomicRanges::GRanges("chr1", IRanges::IPos(c(1,100,200,1500)), "+") ctss <- GenomicRanges::GPos(ctss, stitch = FALSE) ctss <- as(ctss, "CTSS") gr1 <- GenomicRanges::GRanges( "chr1" , IRanges::IRanges(c(650, 650, 1400), 2000), "+") CAGEr:::ranges2annot(ctss, gr1) gr2 <- gr1 gr2$type <- c("transcript", "exon", "transcript") gr2$transcript_type <- c("protein_coding", "protein_coding", "miRNA") CAGEr:::ranges2annot(ctss, gr2)
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