[Bioc-devel] runmean and NA values

[Valerie Obenchain]

'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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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