View source: R/util-binBedpe.R
shiftAnchor | R Documentation |
Define helper function for flexibly shifting an anchor
shiftAnchor(a, p)
a |
GRanges object |
p |
Position within anchors to resize the bin. Can be a character or integer vector of length 1 or length(a) designating the position for each element in bedpe. Character options are "start", "end" and "center". Integers are referenced from the start position for '+' and '*' strands and from the end position for the '-' strand. |
GRanges object with a single position range that has been shifted appropriately.
library(GenomicRanges) ## Create example GRanges gr1 <- GRanges(seqnames = "chr1", ranges = IRanges(start = rep(5000,3), end = rep(6000,3)), strand = c('+', '-', '*')) gr2 <- gr1 |> promoters(upstream = 2000, downstream = 200) ## Shifting anchors by keyword shiftAnchor(gr1, 'start') shiftAnchor(gr1, 'end') shiftAnchor(gr1, 'center') # shiftAnchor(gr1, 'blah') error ## Shifting anchors by position shiftAnchor(gr1, 100) shiftAnchor(gr1, c(100, 200, 300)) # shiftAnchor(gr1, c(100, 200, 300, 400)) error # shiftAnchor(gr1, c(100, 200)) error ## Shifting back to TSS shiftAnchor(gr2, 2000)
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