Check dataset viability per site — data_quality

For each site, checks whether there are enough paired samples (Day 0 + recurrence) with at least one comparable locus to be viable for analysis.

Usage

data_quality_check(
  imported_data,
  min_paired_samples = 10,
  min_comparable_loci = 1,
  verbose = TRUE
)

Arguments

imported_data: Output list from import_data().
min_paired_samples: Minimum paired samples (each with at least min_comparable_loci comparable loci) required per site. Default 10.
min_comparable_loci: Minimum comparable loci a paired sample must have to count toward min_paired_samples. Default 1.
verbose: Logical. Warn for sites that fail the check.

Value

A data frame: Site, n_paired, n_viable_pairs, viable.

Examples

if (FALSE) { # \dontrun{
  data_file <- system.file("extdata", 
                           "Dataset_microsatellite_panel.xlsx", 
                           package = "MalReBay")
  marker_file <- system.file("extdata", 
                             "makers_details.xlsx", 
                             package = "MalReBay")
  imported <- import_data(filepath = data_file, 
                          marker_filepath = marker_file)
  quality  <- data_quality_check(imported)
} # }