amptest-class: Class '"amptest"'

In michbur/chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

Description

An S4 class containing the output amptester function.

Slots

.Data:

"numeric" is a vector containing the fluorescence values.

decisions:

"logical" contains outcomes of various tests. shap.noisy is presence of noise, lrt.test states if data are likely from a amplification curve and both tht.dec and tht.dec defines if the amplification is "positive" or "negative".

noiselevel:

"numeric" user-defined threshold for a significant amplification signal.

background:

range of the background signal in the amplification curve.

polygon:

The pco test determines if the points in an amplification curve (like a polygon) are in a "clockwise" order. The sum over the edges result in a positive value if the amplification curve is "clockwise" and is negative if the curve is counter-clockwise.

slope.ratio:

ratio of the slopes at the start and the end of exponential phase..

Methods

summary

signature(object = "amptest"): prints summary of the object. Silently returns vector of all calculated parameters.

show

signature(object = "amptest"): prints only .Data slot of the object.

plot

signature(object = "amptest"): plots input data and graphical interpretation of link{amptester} tests' results.

Author(s)

Stefan Roediger, Michal Burdukiewicz

See Also

amptester

Examples

# Compare a positive and a negative amplification reaction.
# First simulate positive reaction (fluo.pos) and than the 
# negative reaction (fluo.neg).
# Simulation of an amplifiaction curve with some noise and a high signal.

fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15), 
		      noiselevel = 0.15)

# Plot amplification curve and result of amptester
plot(fluo.pos, xlab = "Cycles", ylab = "RFU", pch = 19, ylim = c(0, 1))
lines(ampt.pos, col = 2, pch = 19, type = "b")
legend(5, 1, c("Raw data", "amptester output"), 
       col = c(1,2,3), bty = "n", pch = c(19, 19))
# Borders for background calculation
abline(v = c(0,15), col = 2)
# Level for background threshold
abline(h = 0.15, col = 3, lty = 2)
text(5, 0.18, "Noise threshold")
# Summary of amptester results 
summary(ampt.pos)

# Simulation of an amplifiaction curve with high noise and a low signal.

fluo.neg <- AmpSim(cyc = 1:40, noise = TRUE, ampl = 0.13, nnl = 0.4)[, 2]
ampt.neg <- amptester(fluo.neg, manual = TRUE, background = c(0, 15), 
		      noiselevel = 0.15)

# Plot amplification curve and result of amptester
plot(fluo.neg, xlab = "Cycles", ylab = "RFU", pch = 19, ylim = c(0, 1))
lines(ampt.neg, col = 2, pch = 19, type = "b")
legend(5, 1, c("Raw data", "amptester output"), 
       col = c(1,2,3), bty = "n", pch = c(19, 19))
# Borders for background calculation
abline(v = c(0,15), col = 2)
# Level for background threshold
abline(h = 0.15, col = 3, lty = 2)
text(5, 0.18, "Noise threshold")
# Summary of amptester results
summary(ampt.neg)
#plot amptester results
plot(ampt.neg)

michbur/chipPCR documentation built on Feb. 28, 2021, 5:57 p.m.