GRangesAnchored class and the
class allow components of a
IRanges (start, end, center)
to be held fixed.
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a Ranges object
Anchoring will fix a Ranges start, end, or center positions,
so these positions will remain the same when performing arithimetic.
GRanges objects, the function
anchor_3p()) will fix the start for the negative strand,
anchor_5p() will fix the end for the
positive strand. Anchoring modifies how arithmetic is performed, for example
modifying the width of a range with
set_width() or stretching a
stretch(). To remove anchoring use
a RangesAnchored object which has the same appearance as a regular Ranges object but with an additional slot displaying an anchor.
Depending on how you want to fix the components of a Ranges, there are
five ways to construct a RangesAnchored class. Here
x is either
anchor_start(x)Fix the start coordinates
anchor_end(x)Fix the end coordinates
anchor_center(x)Fix the center coordinates
anchor_3p(x)On the negative strand fix the start coordinates,
and for positive or unstranded ranges fix the end coordinates.
anchor_5p(x)On the positive or unstranded ranges fix the start coordinates,
coordinates and for negative stranded ranges fix the end coordinates.
To see what has been anchored use the function
This will return a character vector containing a valid anchor.
It will be set to one of
c("start", "end", "center") for an
IRanges object or one of
c("start", "end", "center", "3p", "5p") for a
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df <- data.frame(start = 1:10, width = 5) rng <- as_iranges(df) rng_by_start <- anchor_start(rng) rng_by_start anchor(rng_by_start) mutate(rng_by_start, width = 3L) grng <- as_granges(df, seqnames = "chr1", strand = c(rep("-", 5), rep("+", 5))) rng_by_5p <- anchor_5p(grng) rng_by_5p mutate(rng_by_5p, width = 3L)
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