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
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Computational Biology
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