[Bioc-devel] runmean and NAs

[Hahne, Florian]

Great, thanks a bunch!
-- 






On 7/10/12 10:31 PM, "Valerie Obenchain" <vobencha at fhcrc.org> wrote:

>Hi Florian,
>
>It has been on my TODO and II've just started working on this.
>
>On 07/10/2012 02:19 AM, Hahne, Florian wrote:
>> Hi all,
>> I was asking a while ago whether it would be possible for the runmean
>> function to deal with NA values. Is that still on somebody's radar?
>> Something similar to na.rm would be great. Haven't checked the source
>>code
>> for Rle_runsum yet, but ignoring Nas seems to be a straightforward thing
>> to do. Currently I get
>>
>>> runmean(Rle(c(1:100, NA)), 10)
>> Error in .Call2("Rle_runsum", x, as.integer(k), PACKAGE = "IRanges") :
>>    some values are NA
>>
>>
>> On a related note, why is this not working?
>>> runmean(Rle(c(1:100, Inf)), 10)
>> Error in .Call2("Rle_runsum", x, as.integer(k), PACKAGE = "IRanges")
>> some values are NA, NaN, +/-Inf
>>
>>
>> Shouldn't that simply return Inf for the respective vector elements?
>
>Currently no. The Inf creates a numeric Rle
>
> > Rle(c(1:100, Inf))
>'numeric' Rle of length 101 with 101 runs
>   Lengths:   1   1   1   1   1   1   1   1 ...   1   1   1   1   1
>1   1   1
>   Values :   1   2   3   4   5   6   7   8 ...  94  95  96  97  98  99
>100 Inf
>
>so the code executed is Rle_real_runsum which has this check,
>
>// calculate stat
>if (i == 0) {
>     if (!R_FINITE(*curr_value))
>         error("some values are NA, NaN, +/-Inf");
>
>While I am in there I will address this Inf issue too.
>
>Valerie
>>
>> Thanks,
>> Florian
>>
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>