save_ped_table: Save a '.ped' table to file.

In richelbilderbeek/plinkr: Interface to PLINK

Save a .ped table to file.

Description

Save a .ped table to file to be used by PLINK. Most columns have a single space between them. The exceptions, where there are two spaces between the columns are:

• between sex_code and case_control_code

• between case_control_code and the first SNP

• between each pair of SNPs

Usage

save_ped_table(ped_table, ped_filename)

Arguments

ped_table

a 'pedigree' table. A ped_table is a tibble with these columns: FID The family ID IID Within-family ID (cannot be zero) within_family_id_father Within-family ID of father (0 if father isn't in dataset) within_family_id_mother Within-family ID of mother (0 if mother isn't in dataset) sex_code Sex code (1 = male, 2 = female, 0 = unknown) case_control_code Case control code (1 = control, 2 = case, 9/0/non-numeric = missing data if case/control) snv_[x][y] Nucleotide for the xth variant for haplotype y (y is either a or b) in the .map file (0 = no call) The FID and IID column names match the PLINK names, see https://www.cog-genomics.org/plink/1.9/input#pheno. Use read_plink_ped_file to read a PLINK .ped file. Use check_ped_table to test if a pedigree table is valid.

ped_filename

name of a PLINK .ped file. Use read_plink_ped_file to read a PLINK .ped file.

Author(s)

Richèl J.C. Bilderbeek

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.