Hi, I've found a working solution but not sure whether it's the best one, but could be useful for those who have similar interest : rfq.sf1=append(rfq.sf1[*-n.sf.ids*],rfq.phix1[*n.ph.ids*]) Regards, Ramzi
---------------------------------------------------------------- On Fri, Feb 5, 2010 at 11:53 AM, Ramzi TEMANNI <[email protected]>wrote: > Hi, > I'm trying to generate simulated fastq data by mixing read from original > sample with Phix reads > So i load my sample data and phix data > library(ShortRead) > rfq.sf1<- readFastq(dir, pattern=sample.f1) > rfq.phix1 <- readFastq(dir, pattern=phix.f2) > specify the percentage of reads in the original file to be replaced by phix > reads and select ramdomly the reads to be replaced in sample and the reads > to be selected in phix > nbreads=fx.ratio/100*length(rfq.sf1) > n.sf.ids=sample(1:length(rfq.sf1),nbreads) > n.ph.ids=sample(1:length(rfq.phix1),nbreads) > but when I call > rfq.sf1[n.sf.ids]=rfq.phix1[n.ph.ids] > I get an error > Error in rfq.sf1[n.sf.ids] = rfq.phix1[n.ph.ids] : > object of type 'S4' is not subsettable > I tried then > sread(rfq.sf1[n.sf.ids])=sread(rfq.phix1[n.ph.ids]) > quality(rfq.sf1[n.sf.ids])=quality(rfq.phix1[n.ph.ids]) > And i get an error too > Error in sread(rfq.sf1[n.sf.ids]) = sread(rfq.phix1[n.ph.ids]) : > could not find function "sread<-" > Error in quality(rfq.sf1[n.sf.ids]) = quality(rfq.phix1[n.ph.ids]) : > could not find function "quality<-" > what will be the method to use to replace theses reads ? > Thanks in advance for suggestions. > > > Kind regards > Ramzi > ---------------------------------------------------------------- > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
