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List:       bioc-devel
Subject:    [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?
From:       Rainer Johannes <Johannes.Rainer () eurac ! edu>
Date:       2016-04-30 11:05:22
Message-ID: 9DCB222A-D73E-4EA5-BFCE-08F89335957C () eurac ! edu
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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


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