Reverse IRangesList
Closed this issue · 3 comments
tbrittoborges commented
Is there a vectorized alternative for endoapply(IRangesList, rev)?
x <- IRanges(start = 1:10, width = 3)
group <- c(1,1,2,2,2,3,3,4,4,4)
split_x <- split(x, group)
rev_split_x <- endoapply(split_x, rev)
# works
reverse does not work in this case:
reverse(split_x)
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function ‘reverse’ for signature ‘"CompressedIRangesList"’
hpages commented
Hi,
You can use revElements() for that:
> revElements(split_x)
IRangesList object of length 4:
$`1`
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2 4 3
[2] 1 3 3
$`2`
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 5 7 3
[2] 4 6 3
[3] 3 5 3
$`3`
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 7 9 3
[2] 6 8 3
$`4`
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 10 12 3
[2] 9 11 3
[3] 8 10 3
Note that revElements() has a 2nd argument that lets you specify which list-elements to reverse (by default all elements are reversed). According to the man page (?revElements):
‘revElements(x, i)’ reverses the list elements in ‘x’ specified by ‘i’. It's equivalent to, but faster than, doing ‘x[i] <- endoapply(x[i], rev)’.
We should probably unify reverse() and revElements(), or at least define a reverse() method for list-like objects that calls revElements().
Also note that a good place to find help and ask questions about Bioconductor packages is on our support site.
Best,
H.
tbrittoborges commented
Hi Hervé,
Sorry, I'd missedrevElements in the docs. And thank you for your prompt response, this is what I needed.
Best,
Thiago