Thanks Patrick, that is a sensible schedule. Kasper On Sun, Aug 22, 2010 at 11:37 PM, Patrick Aboyoun <paboyoun at="" fhcrc.org=""> wrote: > ?Kasper, > I'll look to add na.rm arguments to the run* functions by the next release. > > > Cheers, > Patrick > > > On 8/21/10 12:47 PM, Kasper Daniel Hansen wrote: >> >> Thanks a lot for the fix. >> >> Some background. ?I have data associated with (very small) genomic >> locations, irregularly space and I wanted to use the runmeans >> functionality. >> >> Now, for the standard example of Rles: coverage across the genome, >> "missing" data is equal to a coverage of zero. ?But in my case, zero >> is a perfectly fine data value and is quite different from NA which >> indicates no data. ?So while I would like to calculate running means >> with a fixed window size (and hence different number of data points in >> each window since they are irregularly spaced) I could not use the >> runmeans function, with missing values filled in as zero. >> >> I found a solution to my specific problem which uses the fact that my >> problem with the running mean is more about using the right >> denominator. ?I just create 2 Rle's, one with zeroes and data values >> and one with 0 and 1 (1 indicating that there is data) and then the >> "right" running mean is the ratio between two running sums. >> >> Since NA's are allowed I think it makes a lot of sense to support them >> in the run* suite of functions, but it is not something that is >> extremely urgent (to me) (since I found a workaround). >> >> Thanks for the help, >> Kasper >> >> On Fri, Aug 20, 2010 at 8:03 PM, Patrick Aboyoun<paboyoun at="" fhcrc.org=""> >> ?wrote: >>> >>> ?Kasper, >>> I have addressed these two issues, which were caused by inappropriate >>> comparisons using NA_REAL at the C-level for 'numeric' Rle objects. As >>> with >>> the runmed function in the stats package, I don't currently support >>> missing >>> values in the run* methods for Rle objects. Below is the current behavior >>> in >>> IRanges 1.6.15 (BioC 2.6, R-2.11) and IRanges 1.7.21 (BioC 2.7, R-devel). >>> I >>> can add support for missing values. Just so I prioritize this, when do >>> you >>> encounter missing values in your Rle vectors? >>> >>>> tmp = Rle(c(1,2,2,2,3,NA,NA,NA,NA,2,3,3,3,3,3,2)) >>>> tmp >>> >>> 'numeric' Rle of length 16 with 7 runs >>> ?Lengths: ?1 ?3 ?1 ?4 ?1 ?5 ?1 >>> ?Values : ?1 ?2 ?3 NA ?2 ?3 ?2 >>> >>>> runsum(tmp, 3) >>> >>> Error in runsum(tmp, 3) : some values are NA, NaN, +/-Inf >>> >>>> sessionInfo() >>> >>> R version 2.12.0 Under development (unstable) (2010-08-01 r52659) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] IRanges_1.7.21 >>> >>> >>> >>> Patrick >>> >>> >>> On 8/20/10 9:43 AM, Patrick Aboyoun wrote: >>>> >>>> ?Kasper, >>>> I'll take a look into this. The Rle constructor issue seems to be >>>> isolated >>>> to 'numeric' and 'complex' Rles. I'll have an update out soon. >>>> >>>> >>>> Patrick >>>> >>>> >>>> On 8/20/10 8:53 AM, Kasper Daniel Hansen wrote: >>>>> >>>>> Would it make sense to allow missing values in Rle objects and also to >>>>> incorporate removal of missing values in running summaries (and >>>>> possibly other functions)? >>>>> >>>>> Example: >>>>> >>>>>> tmp = Rle(c(1,2,2,2,3,NA,NA,NA,NA,2,3,3,3,3,3,2)) >>>>>> tmp >>>>> >>>>> 'numeric' Rle of length 16 with 10 runs >>>>> ? Lengths: ?1 ?3 ?1 ?1 ?1 ?1 ?1 ?1 ?5 ?1 >>>>> ? Values : ?1 ?2 ?3 NA NA NA NA ?2 ?3 ?2 >>>>> >>>>> Seems like the run of 4 NA's is treated differently >>>>> >>>>>> runsum(tmp, k = 2) >>>>> >>>>> 'numeric' Rle of length 15 with 11 runs >>>>> ? Lengths: ?1 ?2 ?1 ?1 ?1 ?1 ?1 ?1 ?1 ?4 ?1 >>>>> ? Values : ?3 ?4 ?5 NA NA NA NA NA NA NA NA >>>>> >>>>> And there is no way to do runsum(..., na.rm = TRUE) like in sum (as >>>>> far as I can see). >>>>> >>>>> Kasper >>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.12.0 Under development (unstable) (2010-08-20 r52790) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C >>>>> ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 >>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 >>>>> ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C >>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] grid ? ? ?stats ? ? graphics ?grDevices datasets ?utils ? ? methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] multicore_0.1-3 ? IRanges_1.7.19 ? ?matrixStats_0.2.1 >>>>> R.methodsS3_1.2.0 >>>>> [5] ggplot2_0.8.8 ? ? proto_0.3-8 ? ? ? reshape_0.8.3 ? ? plyr_1.1 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.12.0 >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >