Hi, On Tue, Oct 5, 2010 at 2:30 PM, [email protected] <[email protected]> wrote: > Dear bioc-sig-sequencing, > > I would like to work thru the BioC2010 workshop lab, > http://www.bioconductor.org/help/course-materials/2010/BioC2010/Exercises-SimpleRNAseqUseCase.pdf. > > At least three functions and a data set were in a package distributed at the > lab in the package HTSandGeneCentricLabs. > > geneBounds > rpkm > countExonIdsByTxOverlaps > multiplex_export.txt.gz > > Might these functions be incorporated into regular bioconductor packages by > now? Or can you recommend how I might work thru this lab now?
Lots of these can be done with a bit of proficiency with the GenomicFeatures package. For instance, there was a thread from a bit over a week ago that helped the OP get a bit on the way to an RPKM calculation: http://thread.gmane.org/gmane.science.biology.informatics.conductor/31032 I'm not sure what geneBounds is, but I guess you are looking for the txstart/end of genes. You can get there by, for example, loading some test data: R> library(GenomicFeatures) R> txdb_file <- system.file("extdata", "UCSC_knownGene_sample.sqlite", package="GenomicFeatures") R> txdb <- loadFeatures(txdb_file) R> xcripts <- transcriptsBy(txdb, "gene") R> gene.bounds <- lapply(xcripts, range) The rest of your requests should work themselves out within a day or two of getting to know the rest of the GenomicFeatures functionality. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
