Hi everybody I would like to know if there is a way for sub-setting big data.frame of different chromosomes into separate data.frames for the specific chromosomes. I have the results of a microarray experiment in one huge excel sheet. one of the columns is df$Chromosomes I know I can sub-set it using for example: data_9=subset(data,Chromosome=="9") But I would like to know (probably for the next analysis) if there is a way of automating it. Can I, with one command separate my big file into 24 separate data frames (chromosomes 1-22, X,Y)? Thanks Assa [[alternative HTML version deleted]]

The standard practice in Bioconductor with expression data is to manage the information on expression plus information on samples in a unified way in an ExpressionSet. This has many benefits. Were you to do this, you could get chromosome-specific limitation of expression data in various ways. If the data are from a well-annotated chip family, with a standard .db annotation package, say chp.db, you could do, e.g., X9 = X[ get("9", revmap(chpCHR)), ] # use an appropriate chromosome identifier for the package and all the sample information would propagate. If you were not so lucky, but still used expression set structure, you could put the chromosome information in the featureData component, and use X9 = X[ fData(X)$chrom == "9", ] On Mon, Nov 28, 2011 at 9:30 AM, Assa Yeroslaviz <frymor@gmail.com> wrote: > Hi everybody > > I would like to know if there is a way for sub-setting big data.frame of > different chromosomes into separate data.frames for the specific > chromosomes. > > I have the results of a microarray experiment in one huge excel sheet. one > of the columns is df$Chromosomes > I know I can sub-set it using > for example: > data_9=subset(data,Chromosome=="9") > But I would like to know (probably for the next analysis) if there is a way > of automating it. Can I, with one command separate my big file into 24 > separate data frames (chromosomes 1-22, X,Y)? > > Thanks > Assa > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Assa, > Hi everybody > > I would like to know if there is a way for sub-setting big data.frame of > different chromosomes into separate data.frames for the specific > chromosomes. > > I have the results of a microarray experiment in one huge excel sheet. one > of the columns is df$Chromosomes > I know I can sub-set it using > for example: > data_9=subset(data,Chromosome=="9") > But I would like to know (probably for the next analysis) if there is a > way > of automating it. Can I, with one command separate my big file into 24 > separate data frames (chromosomes 1-22, X,Y)? > Try something like split(data, data$Chromosome) HTH \Heidi > Thanks > Assa > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >