calculateAT: Calculate Analytical Threshold

Description

Calculate analytical thresholds estimates.

Usage

calculateAT(data, ref = NULL, block.height = TRUE, height = 500,
  block.sample = TRUE, per.dye = TRUE, range.sample = 20,
  block.ils = TRUE, range.ils = 10, k = 3, rank.t = 0.99,
  alpha = 0.01, ignore.case = TRUE, word = FALSE, debug = FALSE)

Arguments

data

a data frame containing at least 'Dye.Sample.Peak', 'Sample.File.Name', 'Marker', 'Allele', 'Height', and 'Data.Point'.

ref

a data frame containing at least 'Sample.Name', 'Marker', 'Allele'.

block.height

logical to indicate if high peaks should be blocked.

height

integer for global lower peak height threshold for peaks to be excluded from the analysis. Active if 'block.peak=TRUE.

block.sample

logical to indicate if sample allelic peaks should be blocked.

per.dye

logical TRUE if sample peaks should be blocked per dye channel. FALSE if sample peaks should be blocked globally across dye channels.

range.sample

integer to specify the blocking range in (+/-) data points. Active if block.sample=TRUE.

block.ils

logical to indicate if internal lane standard peaks should be blocked.

range.ils

integer to specify the blocking range in (+/-) data points. Active if block.ils=TRUE.

numeric factor for the desired confidence level (method AT1).

rank.t

numeric percentile rank threshold (method AT2).

alpha

numeric one-sided confidence interval to obtain the critical value from the t-distribution (method AT4).

ignore.case

logical to indicate if sample matching should ignore case.

word

logical to indicate if word boundaries should be added before sample matching.

debug

logical to indicate if debug information should be printed.

Value

list of two data frames. The first with result per dye per sample, per sample, globally across all samples, and globally across all samples per dye, for each method. The second is the complete percentile rank list.

Details

Calculate the analytical threshold (AT) according to method 1, 2, and 4 as recommended in the reference by analysing the background signal (noise). Method 1: The average signal + 'k' * the standard deviation. Method 2: The percentile rank method. The percentage of noise peaks below 'rank.t'. Method 4: Utilize the mean and standard deviation and the critical value obtained from the t-distribution for confidence interval 'alpha' (one-sided) and observed peaks analysed (i.e. not blocked) minus one as degrees of freedom, and the number of samples. If samples containing DNA are used a range around the allelic peaks can be blocked from the analysis to discard peaks higher than the noise. Blocking can be within each dye or across all dye channels. Similarily a range around the peaks of the internal lane standard (ILS) can be blocked across all dye channels. Which can bleed-through in week samples (i.e. negative controls) The mean, standard deviation, and number of peaks are calculated per dye per sample, per sample, globally across all samples, and globally across all samples per dye, for each method to estimate AT. Also the complete percentile rank list is calculated.

References