Message-ID: <4FFC912A.3090909@fhcrc.org>
Date: 2012-07-10T20:31:38Z
From: Valerie Obenchain
Subject: [Bioc-devel] runmean and NAs
In-Reply-To: <CC21BFB8.5378%david.heard@novartis.com>
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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