Hi Kamal,
The "rbind" method for SummarizedExperiment objects is defined in the
GenomicRanges package:
> library(GenomicRanges)
> selectMethod("rbind", "SummarizedExperiment")
Method Definition:
function (..., deparse.level = 1)
{
args <- unname(list(...))
.rbind.SummarizedExperiment(args)
}
<environment: namespace:GenomicRanges>
Signatures:
...
target "SummarizedExperiment"
defined "SummarizedExperiment"
And the rbind() generic is defined in the BiocGenerics package:
> rbind
standardGeneric for "rbind" defined from package "BiocGenerics"
function (..., deparse.level = 1)
standardGeneric("rbind")
<environment: 0x1f0b8b0>
Methods may be defined for arguments: ...
Use showMethods("rbind") for currently available ones.
So your package needs to import at least the rbind() generic from
BiocGenerics + I think the method from GenomicRanges:
importFrom(BiocGenerics, rbind)
importMethodsFrom(GenomicRanges, rbind)
I would highly recommend that you actually import *all* the generics
from BiocGenerics:
import(BiocGenerics)
importMethodsFrom(GenomicRanges, rbind)
You also need to put BiocGenerics and GenomicRanges in the Depends field
of your DESCRIPTION file (yes Depends, not Imports -- you can also put
it in both even though some people might try to argue against this).
Please let us know if that still doesn't solve the problem.
Cheers,
H.
On 06/26/2013 07:37 AM, Kamal wrote:
Few more details:
clRes object is essentially a list of SummarizedExperiment class object (of
GenomicRanges package). Each object is of single chromosome since it is
generated by parallelization. I am trying to combine all these object into
a single SummarizedExperiment Object. Since we can combine
SummarizedExperiment objects rowwise by using "rbind", I am combing it
through the function below
chrcomb <- sapply(clRes, function(x) rbind(x))
Error in rbind(x) : no method for coercing this S4 class to a vector
Thanks,
Kamal
On Wed, Jun 26, 2013 at 4:29 PM, Kamal <kamal.fartiya...@gmail.com> wrote:
Prof Brian,
Thanks for the reply. My mistake its "clRes" in place of "result"
chrcomb <- sapply(clRes, function(x) rbind(x))
Error in rbind(x) : no method for coercing this S4 class to a vector
I think what you mentioned about the package forgetting to import an S4
generic for rbind seems the logical explanation of this problem.
Thanks,
Kamal
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