head2tailratio: A function to calculate to head to tail ratio of...

In PCRuniversum/PCRedux: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit

A function to calculate to head to tail ratio of amplification curve data from a quantitative PCR experiment

Description

head2tailratio is a function to calculate the ratio of the head and the tail of a quantitative PCR amplification curve. In this test, only the head (first six cycles) and the tail (last six cycles) form the region of interest (ROI).

Usage

head2tailratio(y, normalize = FALSE, slope_normalizer = FALSE, verbose = FALSE)

Arguments

y	is the cycle dependent fluorescence amplitude (y-axis).
normalize	is a logical parameter, which indicates if the amplification curve.
slope_normalizer	is a logical parameter, which indicates if the head2tailratio should be normalized to the slope of the ROI.
verbose	is a logical parameter, which indicates if all the values, parameters and coefficients of the analysis should be shown.

Value

gives a numeric (S3 class, type of double) as output for the head to tail ratio

Author(s)

Stefan Roediger, Michal Burdukiewcz

Examples

# calculate head to tail ratio on amplification curve data

library(qpcR)

res_head2tailratio <- sapply(2:ncol(competimer), function(i) {
   head2tailratio(y=competimer[, i], normalize=TRUE, slope_normalizer=TRUE)
})

res_head2tailratio_cluster <- kmeans(res_head2tailratio, 3)$cluster

matplot(competimer[, 1], competimer[, -1], xlab="Cycle", ylab="RFU",
        main="competimer data set", type="l", lty=1, col=res_head2tailratio_cluster, lwd=2)

PCRuniversum/PCRedux documentation built on July 30, 2024, 8 p.m.