Hi Dario,
The situation for a GenomicRanges object is no different from the
situation for a IRanges object. In both case, when subject is missing,
the findOverlaps,Vector,missing method is called. This method accepts
the 'drop.self' and 'drop.redundant' arguments thru the ellipsis:
> selectMethod("findOverlaps", c("Vector", "missing"))
Method Definition:
function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
"start", "end", "within", "equal"), select = c("all", "first",
"last", "arbitrary"), ...)
{
.local <- function (query, subject, maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end", "within", "equal"), select =
c("all",
"first", "last", "arbitrary"), ..., drop.self = FALSE,
drop.redundant = FALSE, ignoreSelf = FALSE, ignoreRedundant =
FALSE)
{
if (!identical(ignoreSelf, FALSE) || !identical(ignoreRedundant,
FALSE)) {
.Defunct(msg = wmsg("Please use 'drop.self' and/or
'drop.redundant' instead ",
"of the 'ignoreSelf' and/or 'ignoreRedundant' arguments."))
if (!identical(ignoreSelf, FALSE)) {
if (!identical(drop.self, FALSE))
stop(wmsg("either 'drop.self' or 'ignoreSelf' ",
"can be specified, but not both"))
drop.self <- ignoreSelf
}
if (!identical(ignoreRedundant, FALSE)) {
if (!identical(drop.redundant, FALSE))
stop(wmsg("either 'drop.redundant' or
'ignoreRedundant' ",
"can be specified, but not both"))
drop.redundant <- ignoreRedundant
}
}
select <- match.arg(select)
result <- findOverlaps(query, query, maxgap = maxgap,
minoverlap = minoverlap, type = match.arg(type),
select = "all", ...)
process_self_hits(result, select, drop.self, drop.redundant)
}
.local(query, subject, maxgap, minoverlap, type, select,
...)
}
<environment: namespace:IRanges>
Signatures:
query subject
target "Vector" "missing"
defined "Vector" "missing"
> args(selectMethod("findOverlaps", c("Vector", "missing")))
function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
"start", "end", "within", "equal"), select = c("all", "first",
"last", "arbitrary"), ...)
NULL
Cheers,
H.
On 10/26/2016 03:00 AM, Dario Strbenac wrote:
Good day,
For an IRanges object, findOverlaps has ignoreSelf and ignoreRedundant options.
However, these aren't available for a GenomicRanges input object, even though
the subject parameter is optional and a query GRanges object can be overlapped
with itself. Could this be changed to be consistent?
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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