[Bioc-sig-seq] mapply with GRangesList

[Martin Morgan]

On 03/23/2011 05:00 PM, Dario Strbenac wrote:
  > mapply doesn't iterate over the GRangesList in an example I have that
also uses other types of variables. Would it be possible for it to be
more flexible in this usage ?
>

Hi Dario -- unfortunately mapply 'dispatches' on its '...' argument, and 
'...' dispatch only works when all relevant arguments are of the same 
type (e.g., mapply(function(x, y) print(x), grl, grl) would work). This 
is how S4 is implemented (see ?dotsMethods) so we're kind of stuck with 
this behavior. The workaround is along the lines of

lapply(seq_len(length(grl)),
        function(i, x, y, ...) print(x[[i]]),
        grl, 1:2)

 > mapply
standardGeneric for "mapply" defined from package "IRanges"

function (FUN, ..., MoreArgs = NULL, SIMPLIFY = TRUE, USE.NAMES = TRUE)
standardGeneric("mapply")
<bytecode: 0x207e200>
<environment: 0x20a4cc0>
Methods may be defined for arguments: ...
Use  showMethods("mapply")  for currently available ones.

Martin

> Simple example:
>
> gr1<- GRanges("chr1", IRanges(seq(100, 600, 100), width = 100)) gr2<-
> GRanges("chr2", IRanges(seq(1000, 1600, 100), width = 100)) grl<-
> GRangesList(gr1, gr2)
>
> IRanges::mapply(function(x, y) { print(x) print(y) }, grl, 1:2,
> SIMPLIFY = FALSE)
>
> Result: It keeps using element 1 of grl.
>
> -------------------------------------- Dario Strbenac Research
> Assistant Cancer Epigenetics Garvan Institute of Medical Research
> Darlinghurst NSW 2010 Australia
>
> _______________________________________________ Bioc-sig-sequencing
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