Hi all, I'd like to use the perWindow tool in the girafe package but am working with a genome (maize) that is not accessible through standard annotation packages available through BioC. Does anyone know of an easy way to enter chromosome coordinates directly in perWindow, as this seems to be the only annotation information that is used? Thanks in advance for any advice, Karl Erhard Graduate Student UC Berkeley

Hi Karl, remember that you can always check a function's source code by typing the function name without brackets. You can see that indeed the only organism-related information needed by "perWindow" are the lengths of the individual chromosomes. If there is no organism annotation-package related for your experiment, you can set these chromosome lengths manually, like this: chrlengths(A) <- c("chr1"=2e6, "chr2"=1e6) # etc. i.e., supplying a named numeric vector with those chromosome lengths. The arguments of the function "perWindow", namely "winsize" and "step", then influence how many sliding windows will be computed for the chromosome queried. HTH, Joern On 10/18/2011 09:10 AM, Karl Erhard wrote: > Hi all, > > I'd like to use the perWindow tool in the girafe package but am working > with a genome (maize) that is not accessible through standard annotation > packages available through BioC. > > Does anyone know of an easy way to enter chromosome coordinates directly > in perWindow, as this seems to be the only annotation information that is > used? > > Thanks in advance for any advice, > > Karl Erhard > Graduate Student > UC Berkeley > > _______________________________________________ > 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 -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511