Hello friends, I wanted to know a way to merge all yeilds of FastqStreamer as one ShortReadQ object. Can anybody suggestme a way to do this? readFq <- lapply(paste(inDataPath,fqFiles,sep=""),                         function(fqFiles){                                 fQ <-FastqStreamer(fqFiles,n=1e6)                                 while(length(readsFq <- yield(fQ))){                                        # Collect all chunks                                 }                             return(AllinOneShortReadQ)                         }) Regards, Prashantha [[alternative HTML version deleted]]

On 01/24/2012 05:12 AM, Prashantha Hebbar wrote: > Hello friends, > > I wanted to know a way to merge all yeilds of FastqStreamer as one ShortReadQ object. Can anybody suggestme a way to do this? > > readFq<- lapply(paste(inDataPath,fqFiles,sep=""), > function(fqFiles){ > fQ<-FastqStreamer(fqFiles,n=1e6) > while(length(readsFq<- yield(fQ))){ > # Collect all chunks > } > return(AllinOneShortReadQ) > > }) FastqStreamer returns ShortReadQ objects, these can be appended with append(), but if the objective is to read in a fastq file then use readFastq. Martin > Regards, > Prashantha > [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793