calculateAllele {strvalidator}

Calculate Allele

Description

Calculates summary statistics for alleles per marker over the entire dataset.

Usage

calculateAllele(
  data,
  threshold = NULL,
  sex.rm = FALSE,
  kit = NULL,
  debug = FALSE
)

Arguments

data

data.frame including columns 'Marker' and 'Allele', and optionally 'Height' and 'Size'.

threshold

numeric if not NULL only peak heights above 'threshold' will be considered.

sex.rm

logical TRUE removes all sex markers. Requires 'kit'.

kit

character for the DNA typing kit defining the sex markers.

debug

logical indicating printing debug information.

Details

Creates a table of the alleles in the dataset sorted by number of observations.For each allele the proportion of total observations is calculated. Using a threshold this can be used to separate likely artefacts from likely drop-in peaks. In addition the observed allele frequency is calculated. If columns 'Height' and/or 'Size' are available summary statistics is calculated. NB! The function removes NA's and OL's prior to analysis.

Value

data.frame with columns 'Marker', 'Allele', 'Peaks', 'Size.Min', 'Size.Mean', 'Size.Max', 'Height.Min', 'Height.Mean', 'Height.Max', 'Total.Peaks', 'Allele.Proportion', 'Sum.Peaks', and 'Allele.Frequency'.

See Also

data.table