A function to calculate the slope and intercept of an amplification curve data from a quantitative PCR experiment.

earlyreg is a function to calculate the slope and intercept of an amplification curve data from a quantitative PCR experiment. The number of cycles to be analyzed is defined by the user (default 6 cycles). The output contains the Maximal Information Coefficient (MIC), which can be interpreted as a correlation measure with a range of [0,1]. A value of 0 mean statistically independent data and 1 approaches in "probability for noiseless functional relationships" (see original study by Reshef, D. N. et al. Detecting novel associations in large data sets. Science, 334, 1518-1524 (2011)).

earlyreg(x, y, range = 5, normalize = FALSE)

Arguments

x

is the cycle numbers (x-axis).
y

is the cycle dependent fluorescence amplitude (y-axis).
range

is the number of cycles to be used for the regression.
normalize

is a logical parameter which indicates if the amplification curve data should be normalized to the 99 percent percentile of the amplification curve.

See also

lmrob coefficients

Examples


# Calculate slope and intercept on noise (negative) amplification curve data
# for the cycles 2 to 7 for the C316.amp data set
library(chipPCR)
data(C316.amp)

# Plot the data
plot(C316.amp[, 2], y=C316.amp[, 3], xlab="Cycle", ylab="RFU",
     main="C316.amp data set", lty=1, type="l")
res <- earlyreg(x=C316.amp[, 2], y=C316.amp[, 3], range=5)
res
#>  intercept      slope      sigma 
#> 123.906508 -27.507859   4.414113