score_markers_rev3 {pooledpeaks} | R Documentation |
Score Markers Wrapper
Description
This is a revision of the Fragman script score.markers, for the original instructions and parameters, run '?score.markers'. This revision designates separate parameters for Left and Right search windows.
Usage
score_markers_rev3(
my.inds,
channel = 1,
n.inds = NULL,
panel = NULL,
shift = 0.8,
ladder,
channel.ladder = NULL,
ploidy = 2,
left.cond = c(0.6, 3),
right.cond = 0.35,
warn = FALSE,
windowL = 0.5,
windowR = 0.5,
init.thresh = 200,
ladd.init.thresh = 200,
method = "iter2",
env = parent.frame(),
my.palette = NULL,
plotting = FALSE,
plotdir = "plots_scoring/",
pref = 3
)
Arguments
my.inds |
The list output from the fsa_batch_imp or storing.inds function that contains the channel information from the individuals that you want to score. |
channel |
The number of the channel you wish to analyze. Typically 1 is blue, 2 is green, 3 yellow, and 4 red. |
n.inds |
(optional) A vector specifying which fsa files to score. |
panel |
A vector containing the expected allele sizes for this marker. |
shift |
All peaks at that distance from the tallest peak will be ignored and be considered noise. |
ladder |
A vector containing the expected peaks for your ladder. |
channel.ladder |
The channel number where your ladder can be found. |
ploidy |
The name is a relic of the fact that Fragman::score.markers was originally written for plants. In the context of pooled egg samples it is used to specify the number of possible alleles in the marker. |
left.cond |
The first part is a percentile (0-1) that corresponds to the height that a peak to the left of the tallest peak must be in order to be considered real. The second argument is a number of base pairs that a peak to the left of the tallest peak must be away to be considered as real. |
right.cond |
A percentile (0-1) that corresponds to the height that a peak to the right of the tallest peak must be in order to be real. |
warn |
TRUE/FAlSE Do you want to receive warnings when detecting the ladder? |
windowL |
the window means that all peaks closer by that distance to the left of the panel peaks will be accounted as peaks. |
windowR |
the window means that all peaks closer by that distance to the right of the panel peaks will be accounted as peaks. |
init.thresh |
A value that sets a minimum intensity in order for a peak to be called. |
ladd.init.thresh |
We don't recommend messing with this parameter unless your ladder has special circumstances. See Fragman::score.markers |
method |
In cases where samples weren't sized using the info.ladder.attach function, this technique steps in to identify ladder peaks. You have three method options using an argument: "cor" explores all potential peak combinations and thoroughly searches for correlations to identify the correct peaks corresponding to expected DNA weights; "ci" constructs confidence intervals to identify peaks meeting specified conditions from earlier arguments; "iter2" applies an iterative strategy to identify the most likely peaks aligning with your ladder expectations. The default method is "iter2." |
env |
Please do not change this parameter, it is used to detect the users environment. |
my.palette |
(optional) A character vector specifying which colors to use for the output RFU plots. |
plotting |
TRUE/FALSE Do you want to create pdf output plots? |
plotdir |
The name of the directory where output pdf plots should be stored. |
pref |
The number of plots to be drawn in the output plot. |
Value
The score_markers_rev3 function will return a list containing three variables: $pos, $hei, and $wei. These correspond to the index position for the intensities, the intensity of each peak, and the weight in base pairs based on the ladder respectively. If plotting = TRUE, a pdf file will also have been created in the specified directory. This pdf file allows you to visually inspect how all of the peaks were scored.
Examples
file_path <- system.file("extdata", package = "pooledpeaks")
mock_fsa_batch_imp_output<- fsa_batch_imp(file_path, channels = 5,
fourier = FALSE, saturated = FALSE, lets.pullup = FALSE,
plotting = FALSE, rawPlot = FALSE)
panel <- c(176,179,182,185,188,191,194,197,200,203,206)
ladder <- c( 140, 160, 180, 200, 214, 220,240, 250, 260, 280, 300, 314)
mock_fsa_batch_imp_output <- associate_dyes(mock_fsa_batch_imp_output,
file_path)
score_markers_rev3(my.inds = mock_fsa_batch_imp_output,
channel = 1,
channel.ladder = 5,
panel = "panel",
ladder = ladder,
init.thresh = 200,
ploidy = length(panel),
plotting = FALSE)