amptest-class: Class '"amptest"'

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

Description

An S4 class containing the output amptester function.

Value

An object of amptest class containing result of the test as well as the original data.

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)

chipPCR documentation built on March 5, 2021, 9:06 a.m.