| pullup {Fragman} | R Documentation |
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. |
Details
No major details.
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.
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)
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)