Hi, On Mon, Sep 5, 2011 at 10:22 PM, wang peter <wng.pe...@gmail.com> wrote: > by the way > * Quality assessment > Use ShortRead to produce a basic QA report. Down-sample fastq files if > they are big. > library(ShortRead) > fls <- list.files(fastqDir, "fastq$", full=TRUE) > names(fls) <- sub(".fastq", "", basename(fls)) > ## use FastqSampler if fastq files are large > qas <- lapply(seq_along(fls), > function(i, fls) qa(readFastq(fls[i]), names(fls)[i]), > fls) > qa <- do.call(rbind, qas) > save(qa, file=file.path(outputDir, "qa.rda") > browseURL(report(qa)) > > in the line of qas, i means the ith file. do u need write a loop to assign i
lapply *is* the loop. See ?lapply and ?seq_along Please don't take this the wrong way, but if you feel like you don't really have a good grip on R basics, investing some time to read up on them will really make your life a lot easier ... especially when doing some of the more complicated things that you want to tackle. -steve > thx > shan gao > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing