Thank you Deepayan. What package provides combineLaneReads()?
Ivan ----- Original Message ---- From: Deepayan Sarkar <[email protected]> To: [email protected] Cc: [email protected] Sent: Thursday, 23 April, 2009 16:37:57 Subject: Re: [Bioc-sig-seq] Input from multiple Solexa runs On Thu, Apr 23, 2009 at 12:24 PM, <[email protected]> wrote: > > Hello, > > How do you pool together reads from multiple Solexa runs? > > Specificaly: > > Say that the structure of my hard drive looks like this > > /experiment01/GERALD_analysis01/(here all 8 lanes) > /experiment01/GERALD_analysis02/(here all 8 lanes) > /experiment02/GERALD_analysis01/(here all 8 lanes) > > Now say that my control1 lanes are in > experiment01, analysis01, lanes 1 and 2 > experiment01, analysis02, lanes 3 and 4 > (all four lanes are biologically identical) > > Now say that my treatment1 is in > experiment02, analysis01, lane 5 and 7 > > Now say that I plan to read all Reads with a filter instance called myFilter. > > The question: > > How do I collect all that information into a single GenomeDataList object > where I can call its GenomeData objects like this > myGenomeDataList$control1 > myGenomeDataList$treatment1 > ? > > Please try to answer the specific example because there is no alternative > documentation. The function you are looking for is 'combineLaneReads'. If x is a GenomeDataList, then combineLaneReads(x) will give you a GenomeData object combining all reads in x. Additionally, you can treat a GenomeDataList object like a list, in the sense that you can subset them using [, combine them using c(), and changes their names using names()<-. So, let's say your per-run data are in variables called expt1_analysis1 expt1_analysis2 expt2_analysis1 which are all GenomeDataList objects with names "1", "2", ..., "8" (I assume you know how to do this; as we discussed this a few days back). Then, the usage would be: control1 <- combineLaneReads(c(expt1_analysis1[c("1", "2")], expt1_analysis2[c("3", "4")])) treatment1 <- combineLaneReads(expt2_analysis1[c("5", "7")]) (these would both be GenomeData objects). To combine them into a GenomeDataList, simply do myGenomeDataList <- GenomeDataList(list(control1 = control1, treatment1 = treatment1)) or combining the two steps: myGenomeDataList <- GenomeDataList(list(control1 = combineLaneReads(c(expt1_analysis1[c("1", "2")], expt1_analysis2[c("3", "4")])), treatment1 = combineLaneReads(expt2_analysis1[c("5", "7")]))) -Deepayan _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
