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setMethod(
f="plotNtFrequency",
signature= signature(x="ShortRead"),
definition = function(x,...) {
nt <- t(alphabetByCycle(sread(x)))
nt <- nt[,c("A","C","G","T","N")]
nt <- t(scale(t(nt), center=FALSE, scale=rowSums(nt)))
matplot(nt, xlab = "Cycle", ylab = "Nt frequency", type = "l", lty=1, col=1:5, ...)
abline(h=1/4, col="gray")
legend("topright",colnames(nt), fill=1:5,bg="white")
}
)
setMethod(
f = "boxplot",
signature = signature(x="FastqQuality"),
definition = function(x,...) {
bp <- as.data.frame(as(x,"matrix"))
colnames(bp) <- as.character(1:NCOL(bp))
boxplot(bp,...)
}
)
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