pooledpeaks (version 1.1.1)

score_markers_rev3: 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
)

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.

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.

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)