Fragman (version 1.0.9)

pullup: Applying pullup to channels/colors

Description

This function takes a matrix of DNA intensities and merge all the channels (columns) to identify overall peaks and then creates a window moving from peak to peak looking for the channel where this peak is real and adjust the intensities in the other channels.

Usage

pullup(mati, plotting=FALSE, channel=4)

Arguments

mati

matrix of intensities where each column is a channel/color for a given sample.

plotting

a TRUE/FALSE value indicating if the results from adjusting the intensities should be drawn or not.

channel

a numeric value indicating which of the channles/color (column) allocates the ladder intensties.

Value

If arguments are correctly specified the function returns:

mati

A new matrix of DNA intensities corrected for overlapping of wavelenth readings in different channels.

Details

No major details.

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

# NOT RUN {
data(my.plants)
layout(matrix(1:2,2,1))
# without pull up adjustment
plot(my.plants[[1]][,1], type="l", col="blue", xlim=c(2750,2850))
lines(my.plants[[1]][,2], col="green")
lines(my.plants[[1]][,3], col="gold")
## adjusted
yy <- pullup(my.plants[[1]])
plot(yy[,1], type="l", col="blue", xlim=c(2750,2850))
lines(yy[,2], col="green")
lines(yy[,3], col="gold")
# general view
yy1 <- pullup(my.plants[[1]], plotting=TRUE)
# }