Import multiple genotype datasets from a list of configurations

Reads and imports multiple genotype datasets specified in a list of configurations. Each configuration must include the path to the genotype data and information on field mapping. Optionally, you can also specify codes, quality threshold, separator, lines to skip, and a subset of IDs to retain. The function automatically fills the `xref_path` slot per individual and combines maps into a single data.frame, adding a `SourcePath` column indicating their origin and removing duplicated SNP rows (by Name). Prints progress messages indicating the current path being loaded (with counter).

import_geno_list(config_list)

Arguments

config_list

A list of configuration lists. Each element should contain: - `path` (character): Path to the genotype file or folder. - `fields` (list): Named list defining the columns (e.g., SNP ID, sample ID, alleles, confidence). - `codes` (character vector, optional): Allele codes (default is c("A", "B")). - `threshold` (numeric, optional): Maximum allowed missingness or confidence threshold (default 0.15). - `sep` (character, optional): Field separator in the input file (default "tab-delimited"). - `skip` (integer, optional): Number of lines to skip at the beginning of the file (default 0). - `verbose` (logical, optional): Whether to print detailed messages (default TRUE). - `subset` (character vector, optional): Vector of sample IDs to retain after import.

Value

An object of class `SNPDataLong` containing: - Combined genotype matrix (`geno`). - Combined map (`map`) as a single data.frame with `SourcePath` column and without duplicated rows. - Combined `xref_path` vector (one entry per individual). - `path` slot as a semicolon-separated string of all input dataset paths.