calculateCopies {strvalidator}

Calculate Allele Copies

Description

Calculates the number of alleles in each marker.

Usage

calculateCopies(
  data,
  observed = FALSE,
  copies = TRUE,
  heterozygous = FALSE,
  debug = FALSE
)

Arguments

data

Data frame containing at least columns 'Sample.Name', 'Marker, and 'Allele*'.

observed

logical indicating if a column 'Observed' should be used to count the number of unique alleles.

copies

logical indicating if a column 'Copies' should be used to indicate the number of allele copies with 1 for heterozygotes and 2 for homozygotes.

heterozygous

logical indicating if a column 'Heterozygous' should be used to indicate heterozygotes with 1 and homozygotes with 0.

debug

logical indicating printing debug information.

Details

Calculates the number of unique values in the 'Allele*' columns for each marker, the number of allele copies, or indicate heterozygous loci. Observed - number of unique alleles. Copies - number of allele copies, '1' for heterozygotes and '2' for homozygotes. Heterozygous - '1' for heterozygous and '0' for homozygous loci. NB! The 'copies' and 'heterozygous' option are intended for known complete profiles, while 'observed' can be used for any samples to count the number of peaks. Sample names must be unique. The result is per marker but repeated for each row of that marker. Data in 'fat' format is auto slimmed.

Value

data.frame the original data frame with optional columns 'Observed', 'Copies', and 'Heterozygous'.