Dear R user, I have a matrix like: ID group1 group2 group3 s1 0 2 3 s2 1 0 4 s1 3 4 1 s4 2 2 0 I would like to sum the values with same ID to have the matrix as below: ID group1 group2 group3 s1 3 6 4 s2 1 0 4 s4 2 2 0 I checked aggregate() may help to complete this job, but unfortunately I have the error message when I do this. > all.data <- read.csv("test.csv") > aggregate(group1 ~ ID, data=all.data, FUN=sum) Error in eval(expr, envir, enclos) : object 'ID' not found Please help me to generate the sum for the matrix. It's been appreciated for any help. Thanks a lot -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-5 vegan_2.0-10 lattice_0.20-24 permute_0.8-0 Heatplus_2.6.0 gplots_2.12.1 loaded via a namespace (and not attached): [1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 grid_3.0.2 gtools_3.1.1 KernSmooth_2.23-10 tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.

Hi anonymous guest, On 03/06/2014 01:43 PM, guest [guest] wrote: > > Dear R user, Note that this is the Bioconductor mailing list. Looks like your question is a general question R question, not a Bioconductor specific one. > > I have a matrix like: > > ID group1 group2 group3 > s1 0 2 3 > s2 1 0 4 > s1 3 4 1 > s4 2 2 0 > > I would like to sum the values with same ID to have the matrix as below: > ID group1 group2 group3 > s1 3 6 4 > s2 1 0 4 > s4 2 2 0 > > I checked aggregate() may help to complete this job, but unfortunately I have the error message when I do this. > >> all.data <- read.csv("test.csv") Note that 'all.data' is a data.frame, not a matrix. >> aggregate(group1 ~ ID, data=all.data, FUN=sum) > Error in eval(expr, envir, enclos) : object 'ID' not found Trying with a matrix: m <- matrix(sample(12L), ncol=3) ID <- c("s1", "s2", "s1", "s4") rownames(m) <- ID colnames(m) <- paste0("group", 1:3) Then: > m group1 group2 group3 s1 1 9 7 s2 11 12 10 s1 2 5 6 s4 8 3 4 > aggregate(group1 ~ ID, data=m, FUN=sum) ID group1 1 s1 3 2 s2 11 3 s4 8 aggregate() will probably be too slow anyway on a matrix with many many rows (hundreds of thousands or more). Here is a faster solution that leverages the IRanges infrastructure: library(IRanges) m2 <- apply(m, 2, function(x) sum(splitAsList(x, ID))) Cheers, H. PS: IRanges is a Bioconductor package. > > Please help me to generate the sum for the matrix. It's been appreciated for any help. > > Thanks a lot > > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RColorBrewer_1.0-5 vegan_2.0-10 lattice_0.20-24 permute_0.8-0 Heatplus_2.6.0 gplots_2.12.1 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 grid_3.0.2 gtools_3.1.1 KernSmooth_2.23-10 tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319