RangesList-utils {IRanges} | R Documentation |
Utility functions for manipulating RangesList
objects.
## S4 method for signature 'RangesList': gaps(x, start=NA, end=NA) ## S4 method for signature 'RangesList': reduce(x, with.inframe.attrib = FALSE) ## S4 method for signature 'RangesList': range(x, ..., na.rm = FALSE)
x |
A RangesList |
start |
The start of the range over which to calculate the
gaps. If NA , use the minimum start position in the
Ranges object. |
end |
The end of the range over which to calculate the gaps. If
NA , use the maximum end position in the Ranges
object. |
with.inframe.attrib |
Ignored. |
... |
Additional RangesList objects |
na.rm |
Ignored |
The gaps
function takes the complement (the gaps
)
of each element in the list and returns the result as a
RangesList
.
The reduce
method merges (via reduce
) all of the
elements into a single Ranges
object and returns the result
as a length-one RangesList
.
range
finds the range
, i.e.
a Ranges
with one range, from the minimum start to the maximum
end, on each element in x
and returns the result as a
RangesList
. If there are additional RangesList
objects
in ...
, they are merged into x
by name, if all objects
have names, otherwise, if they are all of the same length, by
position. Else, an exception is thrown.
A RangesList
object. For gaps
and range
, length
is the same as that of x
. For reduce
, length is one.
Michael Lawrence, H. Pages
# 'gaps' range1 <- IRanges(start=c(1,2,3), end=c(5,2,8)) range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5)) collection <- RangesList(one = range1, range2) # these two are the same RangesList(gaps(range1), gaps(range2)) gaps(collection) # 'reduce' range2 <- IRanges(start=c(45,20,1), end=c(100,80,5)) collection <- RangesList(one = range1, range2) # and these two are the same reduce(collection) RangesList(asNormalIRanges(IRanges(c(1,20), c(8, 100)), force=FALSE)) # 'range' rl <- RangesList(a = IRanges(c(1,2),c(4,3)), b = IRanges(c(4,6),c(10,7))) rl2 <- RangesList(c = IRanges(c(0,2),c(4,5)), a = IRanges(c(4,5),c(6,7))) range(rl, rl2) # matched by names names(rl2) <- NULL range(rl, rl2) # now by position