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Question: IRanges::Rle and missing values
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gravatar for Kasper Daniel Hansen
7.3 years ago by
United States
Kasper Daniel Hansen6.3k 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
ADD COMMENTlink modified 7.3 years ago by Patrick Aboyoun1.6k • written 7.3 years ago by Kasper Daniel Hansen6.3k
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gravatar for Patrick Aboyoun
7.3 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k 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
ADD COMMENTlink written 7.3 years ago by Patrick Aboyoun1.6k
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
ADD REPLYlink written 7.3 years ago by Patrick Aboyoun1.6k
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 > >
ADD REPLYlink written 7.3 years ago by Kasper Daniel Hansen6.3k
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 >>
ADD REPLYlink written 7.2 years ago by Patrick Aboyoun1.6k
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 >>> > >
ADD REPLYlink written 7.2 years ago by Kasper Daniel Hansen6.3k
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