Fragman (version 1.0.1)

overview2: Assesing several plants with an overview

Description

This function uses information from the FSA files read from storing.inds function and creates an overlapping plot to assess graphically the peaks of several plants in certain channel in order to create a panel for the next functions score.easy. The function contains several defaults in most of the arguments, please check arguments but in general.

Please! once you have found the best parameters for the arguments to match your ladder using the detect.ladder function, please pass those values to this function since it will use the same function internally and your dna sizes will depend on that, please make sure the 'dev' argument is passed to the new functions.

Usage

overview2(my.inds, cols = 1, n.inds = NULL, xlim = NULL, 
        ylim = NULL, ladder, channel.ladder = NULL, ploidy = 2, 
        ci.upp = 1.96, ci.low = 1.96, dev = 50, method="cor", 
        init.thresh=200, ladd.init.thresh=200, lwd=.1, warn=TRUE, 
        min.panel=100, env = parent.frame())

Arguments

my.inds

List with the channels information from the individuals specified, usually coming from the storing.inds function output

cols

The channel/color you wish to analyze, usually 1 is blue, 2 is green, 3 is yellow, 4 is red and so on

n.inds

Vector specifying the plants to be scored

xlim

A vector containing the base pair interval where the plot should be drawn

ylim

A vector containing the intensity interval where the plot should be drawn

ladder

A vector containing the expected weights for the ladder peaks that will be found the using the find.ladder function

channel.ladder

A scalar value indicating in which channel or color the ladder was read

ploidy

A scalar value indicating the ploidy of the organism to be scored

ci.upp

A scalar value indicating how many standar errors will be used to detect peaks when checking the height of the ladder peaks(upper bound). To be used in the find.ladder function

ci.low

A scalar value indicating how many standar errors will be used to detect peaks when checking the height of the ladder peaks(lower bound). To be used in the find.ladder function

dev

A scalar value indicating the number of indexes to be used as peak separation when deciding the ladder peaks, for more details check find.ladder function

method

An argument indicating one of the 2 methods available; "cor" makes all possible combination of peaks and searches exhaustive correlations to find the right peaks corresponsding to the expected DNA weights, or "ci" constructing confidence intervals to look

init.thresh

An initial value of intensity to detect peaks. We recommend not to deal to much with unless you have highly controlled dna concentrations in your experiment

ladd.init.thresh

A value of intensity to detect peaks in the internal use of the find.ladder function. We recommend not to deal to much with it unless you identified special situations with your ladder

lwd

The width of the line

warn

A TRUE/FALSE value indicating if warnings should be provided when detecting the ladder

min.panel

A scalar value indicating which peak values should be ignored when creating a panel. If 'xlim' values are specified the 'min.panel' value is ignored and instead the panel peaks provided by the program are based in the region where you are zooming in.

env

this is used to detect the environment of the user and load the result in the same environment.

Value

• If rarguments are correct the function returns a list containing [object Object],[object Object]

Details

No major details.

References

We have spent valuable time developing this package, please cite it in your publication:

Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Salazar W, Zalapa J. (2015) Fragma: An R package for fragment analysis. R package version 1.0. URL https://cran.r-project.org/web/packages/Fragman/.

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)
my.plants <- my.plants[1]
my.ladder <- c(120, 125, 129, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375)
overview2(my.inds=my.plants, cols = 1, ladder=my.ladder, lwd=1)
# now use:
# my.panel <- locator(type="p", pch=20, col="red")$x
# to click over the peaks and get the sizes in base pairs
# when you are done make sure you press the "Esc" key, do not push the stop button