[Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

[Hervé Pagès]

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
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
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: hpages at fredhutch.org
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