[Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

[Rainer Johannes]

Dear all,

I was wondering, you think it would be possible to make the transcriptLength function in GenomicFeatures a method and export that? Reason is that I have also implemented a transcriptLength function (actually presently a method in order to allow that to be used for EnsDb and TxDb objects), but this causes the warning

The following object is masked from 'package:GenomicFeatures':

    transcriptLengths

on package loading.

Just in case, that’s the code from my package:

if(!isGeneric("transcriptLengths"))
    setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
                                             with.utr5_len=FALSE,
                                             with.utr3_len=FALSE, ...)
        standardGeneric("transcriptLengths”))
setMethod("transcriptLengths", "EnsDb", function(x, with.cds_len=FALSE, with.utr5_len=FALSE,
                                                with.utr3_len=FALSE, filter=list()){
    return(.transcriptLengths(x, with.cds_len=with.cds_len, with.utr5_len=with.utr3_len,
                              with.utr3_len=with.utr3_len, filter=filter))
})


cheers, jo