On 8/13/12 9:58 PM, "Valerie Obenchain" <vobencha at fhcrc.org> wrote:
>'na.rm' has been added to runwtsum() and runq() in IRanges 1.15.33.
>
>Valerie
>
>
>On 08/06/2012 10:44 AM, Valerie Obenchain wrote:
>> Florian, Kasper,
>>
>> In IRanges 1.15.26, runsum() and runmean() now have an 'na.rm' argument,
>>
>> x <- Rle(c(2, 1, NA, 3, 1))
>> > runsum(x, k=2, na.rm=TRUE)
>> numeric-Rle of length 4 with 4 runs
>> Lengths: 1 1 1 1
>> Values : 3 1 3 4
>>
>> > runsum(x, k=2, na.rm=FALSE)
>> numeric-Rle of length 4 with 3 runs
>> Lengths: 1 2 1
>> Values : 3 NA 4
>>
>> > runmean(x, k=2, na.rm=TRUE)
>> numeric-Rle of length 4 with 4 runs
>> Lengths: 1 1 1 1
>> Values : 1.5 1 3 2
>>
>> > runmean(x, k=2, na.rm=FALSE)
>> numeric-Rle of length 4 with 3 runs
>> Lengths: 1 2 1
>> Values : 1.5 NA 2
>>
>> Is it worth adding the argument to runmed(), runwtsum() and runq() as
>> well? I'm not sure how heavily used these functions are.
>>
>> Valerie
>>
>>
>> On 04/13/2012 02:36 PM, Valerie Obenchain wrote:
>>> Hi Florian,
>>>
>>> Thanks for the reminder. I can pick this up and will post back here
>>> when it's done.
>>>
>>> Valerie
>>>
>>>
>>> On 04/13/2012 08:06 AM, Hahne, Florian wrote:
>>>> Hi all,
>>>> Runmean and the related run* functions currently can't deal with NA
>>>> values. Kasper asked for a na.rm argument a long while ago and back
>>>> then
>>>> Patrick agreed to add this in one of the upcoming releases
>>>> (https://stat.ethz.ch/pipermail/bioconductor/2010-August/034982.html)
>>>>
>>>> Is that still on someone's radar? I would really like to see that in
>>>> runmean for the same reasons Kasper pointed out: NAs and zeros are not
>>>> necessarily equivalent in Rle vectors, and I would like to be able to
>>>> smooth data that contains NAs.
>>>>
>>>> Thanks,
>>>> Florian
>>>>
>>>>
>>>> Florian Hahne
>>>> Novartis Institute For Biomedical Research
>>>> Translational Sciences / Preclinical Safety / PCS Informatics
>>>> Expert Data Integration and Modeling Bioinformatics
>>>> CHBS, WKL-135.2.26
>>>> Novartis Institute For Biomedical Research, Werk Klybeck
>>>> Klybeckstrasse 141
>>>> CH-4057 Basel
>>>> Switzerland
>>>> Phone: +41 61 6967127
>>>> Email : florian.hahne at novartis.com
>>>>
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
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>