qual <- PhredQuality(quality(quality(reads)));#1 qual <- FastqQuality(quality(quality(reads)));#2 readM <- as(qual, "matrix"); pdf(file="boxplot.pdf",width=25, height = 75); # Save box plot as boxplot.pdf in current folder boxplot(as.data.frame((readM)), outline = FALSE, main="Per Cycle Read Quality", xlab="Cycle", ylab="Phred Quality"); # build per cycle boxplot dev.off()
i wrote such coding,because PhredQuality and FastqQuality have the same information those coding can run well on windows but the #1 cannot run well on linux and gave such error > qual <- PhredQuality(quality(quality(reads))); > readM <- as(qual, "matrix"); Error in as.vector(data) : no method for coercing this S4 class to a vector [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing