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
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