This function processes one or more sparse relationship components (additive, mitochondrial, and common nuclear) and converts them into kinship link pairs. The resulting related pairs are either returned as a data frame or written to disk in CSV format.
Usage
com2links(
rel_pairs_file = "dataRelatedPairs.csv",
ad_ped_matrix = NULL,
mit_ped_matrix = mt_ped_matrix,
mt_ped_matrix = NULL,
cn_ped_matrix = NULL,
write_buffer_size = 1000,
update_rate = 1000,
gc = TRUE,
writetodisk = TRUE,
verbose = FALSE,
legacy = FALSE,
outcome_name = "data",
drop_upper_triangular = TRUE,
...
)Arguments
- rel_pairs_file
File path to write related pairs to (CSV format).
- ad_ped_matrix
Matrix of additive genetic relatedness coefficients.
- mit_ped_matrix
Matrix of mitochondrial relatedness coefficients. Alias:
mt_ped_matrix.- mt_ped_matrix
Matrix of mitochondrial relatedness coefficients.
- cn_ped_matrix
Matrix of common nuclear relatedness coefficients.
- write_buffer_size
Number of related pairs to write to disk at a time.
- update_rate
Numeric. Frequency (in iterations) at which progress messages are printed.
- gc
Logical. If TRUE, performs garbage collection via
gcto free memory.- writetodisk
Logical. If TRUE, writes the related pairs to disk; if FALSE, returns a data frame.
- verbose
Logical. If TRUE, prints progress messages.
- legacy
Logical. If TRUE, uses the legacy branch of the function.
- outcome_name
Character string representing the outcome name (used in file naming).
- drop_upper_triangular
Logical. If TRUE, drops the upper triangular portion of the matrix.
- ...
Additional arguments to be passed to
com2links