transfft: Applying the fourier transformation to a data frame

In Fragman: Fragment Analysis in R

Description

This function takes a vector and applies a fourier transformation in order to smooth the peaks usinf the fft function in the base package. Use only top 40 percent of the lowest frequencies.

Usage

transfft(sn, top=0.3)

Arguments

sn	a numeric vector containing the DNA intensities for the capillary electrophoresis.
top	percent of lowest frequencies that should be used for the fourier transformation.

Details

No major details.

Value

If arguments are correctly specified the function returns:

$y

A new vector of DNA intensities smoothed to avoid extra noisy peaks.

References

Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Salazar W, Zalapa J. Fragman: An R package for fragment analysis. 2016. BMC Genetics 17(62):1-8.

Robert J. Henry. 2013. Molecular Markers in Plants. Wiley-Blackwell. ISBN 978-0-470-95951-0.

Ben Hui Liu. 1998. Statistical Genomics. CRC Press LLC. ISBN 0-8493-3166-8.

Examples

data(my.plants)
g1 <- transfft(my.plants[[1]][,4], top=0.8)
g2 <- transfft(my.plants[[1]][,4], top=0.4)
g3 <- transfft(my.plants[[1]][,4], top=0.1)
layout(matrix(1:3,3,1))
plot(g1, type="l")
lines(g2, col="red")
lines(g3, col="blue")
par1 <- c("top=0.8", "top=0.4", "top=0.1")
par2 <- c("black", "red", "blue")
par3 <- c(1,1,1)
legend("topright", legend=par1, col=par2, bty = "n", lty=par3, lwd=par3, cex=0.75)

Example output

Fragman documentation built on May 2, 2019, 8:26 a.m.