| solveUserSEW {IRanges} | R Documentation |
solveUserSEW is a utility function that solves a set of
user-supplied start/end/width values.
solveUserSEW(refwidths, start=NA, end=NA, width=NA,
translate.nonpositive.coord=TRUE,
allow.nonnarrowing=FALSE)
refwidths |
Vector of non-negative integers containing the reference widths. |
start, end, width |
Vectors of integers, eventually with NAs, containing the set of user-supplied start/end/width values. |
translate.nonpositive.coord, allow.nonnarrowing |
TRUE or FALSE.
|
start, end and width must have the same number of
elements as, or less elements than, refwidths. In the latter case,
they are expanded cyclically to the length of refwidths (provided
none are of zero length). After this expansion, each row in the 3-column
matrix obtained by binding those 3 vectors together must contain at least
one NA (otherwise an error is returned).
Then each row is "solved" i.e. the 2 following transformations are
performed (i is the indice of the row):
(1) if translate.nonpositive.coord is TRUE then a
non-positive value of start[i] or end[i] is
considered to be a -refwidths[i]-based coordinate so
refwidths[i]+1 is added to it to make it 1-based;
(2) the NAs in the row are treated as unknowns which values are deduced
from the known values in the row and from refwidths[i].
The exact rules for (2) are the following.
Rule (2a): if the row contains at least 2 NAs, then width[i] must be
one of them (otherwise an error is returned), and if start[i] is one
of them it is replaced by 1, and if end[i] is one of them it is
replaced by refwidths[i], and finally width[i] is replaced by
end[i] - start[i] + 1.
Rule (2b): if the row contains only 1 NA, then it is replaced by the solution
of the width[i] == end[i] - start[i] + 1 equation.
Finally, the set of solved rows is returned as an IRanges object.
An IRanges object (with the same number of elements as
refwidths) representing the set of solved start/end/width values,
or an error if either (1) the set of user-supplied start/end/width values
is invalid or (2) allow.nonnarrowing is FALSE and the ranges
represented by the solved start/end/width values are not narrowing
the ranges represented by the user-supplied start/end/width values.
H. Pages
refwidths <- c(5:3, 6:7) refwidths solveUserSEW(refwidths) solveUserSEW(refwidths, start=4) solveUserSEW(refwidths, end=3, width=2) solveUserSEW(refwidths, start=-3) solveUserSEW(refwidths, start=-3, width=2) solveUserSEW(refwidths, end=-4) ## The start/end/width arguments are expanded cyclically solveUserSEW(refwidths, start=c(3, -4, NA), end=c(-2, NA))