Description Usage Arguments Value Author(s) References Examples
MFIaggr is used for a fast multiple comparison of the cycle dependent variance of the fluorescence.
1 2 3 4 5 6 7 8 9 | ## S4 method for signature 'numeric,numeric'
MFIaggr(x, y, cyc = 1, fluo = 2:ncol(x),
RSD = FALSE, rob = FALSE, llul = c(1,10))
## S4 method for signature 'matrix,missing'
MFIaggr(x, y, cyc = 1, fluo = 2:ncol(x),
RSD = FALSE, rob = FALSE, llul = c(1,10))
## S4 method for signature 'data.frame,missing'
MFIaggr(x, y, cyc = 1, fluo = 2:ncol(x),
RSD = FALSE, rob = FALSE, llul = c(1,10))
|
x |
is the column of a data frame for the cycle or data.frame/matrix with whole data. |
y |
are multiple columns of fluorescence values from a
|
cyc |
is the index of column containing the cycle data.
Used only if |
fluo |
are the columns containing the fluorescence data.
Used only if |
RSD |
Setting the option |
rob |
Using the option |
llul |
is a parameter to define the lower and upper data limit (cycle), aka region of interest (ROI) used for the density and quantile plot. |
An object of the class refMFI
. refMFI means referenced
Mean Fluorescence Intensity (Roediger et al. 2013).
Stefan Roediger, Michal Burdukiewicz
Roediger S, Boehm A, Schimke I. Surface Melting Curve Analysis with R. The R Journal 2013;5:37–53.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | # First Example
# Cycle dependent variance of the refMFI using standard measures
# (Mean, Standard Deviation (SD)).
# Use Standard Deviation (SD) in the plot
data(VIMCFX96_60)
MFIaggr(VIMCFX96_60[, 1], VIMCFX96_60[, 2:ncol(VIMCFX96_60)])
#alternative usage
MFIaggr(VIMCFX96_60)
#only second and forth column
plot(MFIaggr(VIMCFX96_60, fluo = c(2, 4)))
# Example
# Use of MFIaggr to test for heteroskedasticity using the Breusch-Pagan
# test. The data were aggregated with the MFIaggr function and assigned to
# the object res. The standard deviation was transformed to the variance.
# The plot shows the cycle dependent variance.
# First cycles 1 to 10 of 96 qPCR replicate amplification curves were
# analyzed. Next the cycles 1 to 40 of the same amplification curve data
# were analyzed. The Breusch-Pagan confirmed the heteroskedasticity in the
# amplification curve data.
default.par <- par(no.readonly = TRUE)
par(mfrow = c(1,2), bty = "n")
res <- MFIaggr(VIMCFX96_60[, 1], VIMCFX96_60[, 2:ncol(VIMCFX96_60)],
llul = c(1,10))
head(res)
plot(res[, 1], res[, 3]^2, xlab = "Cycle", ylab = "Variance of refMFI",
xlim = c(1,10), main = "ROI from Cycle 1 to 10", pch = 19, type = "b")
abline(v = c(1,10), col = "grey", lty = 2, lwd = 2)
legend("top", paste0("Breusch-Pagan test p-value: \n", format(summary(res)[5],
digits = 2)), bty = "n")
res <- MFIaggr(VIMCFX96_60[, 1], VIMCFX96_60[, 2:ncol(VIMCFX96_60)],
llul = c(1,40))
head(res)
plot(res[, 1], res[, 3]^2, xlab = "Cycle", ylab = "Variance of refMFI",
main = "ROI from Cycle 1 to 40", pch = 19, type = "b")
abline(v = c(1,40), col = "grey", lty = 2, lwd = 2)
legend("top", paste0("Breusch-Pagan test p-value: \n", format(summary(res)[5],
digits = 2)), bty = "n")
par(default.par)
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