On Thu, Apr 23, 2009 at 2:05 PM, <[email protected]> wrote: > > Thank you Deepayan. > > What package provides combineLaneReads()?
chipseq > > 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
