create_plink_text_data: Create a set of 'PLINK' textual data

In richelbilderbeek/plinkr: Interface to PLINK

Create a set of PLINK textual data

Description

Create a set of PLINK textual data

Usage

create_plink_text_data(map_table, ped_table)

Arguments

map_table

a genetic mapping table. A map_table is a tibble with the following columns: CHR: the chromosome code or contig name. The chromosome number cannot exceed 95 (https://www.cog-genomics.org/plink/1.9/input#chr_set) SNP: Variant identifier position_cm: Position in morgans or centimorgans. This value is optional. Zeroes denote it is unused BP: Base-pair coordinat Use read_plink_map_file to read a PLINK .map file. Use check_map_table to test if a genetic mapping table is valid.

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.

Author(s)

Richèl J.C. Bilderbeek

Examples

create_plink_text_data(
  map_table = get_test_map_table(),
  ped_table = get_test_ped_table()
)

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