create_phe_table_from_ped_table: Create a single-phenotype table from pedigree ('.ped') table

In richelbilderbeek/plinkr: Interface to PLINK

Create a single-phenotype table from pedigree (.ped) table

Description

Create a single-phenotype table from pedigree (.ped) table. The individuals' family and within-family ID's are copied. The case_control_code is copied as well, but renamed to trait and divided by then. In this way, PLINK treats the phenotype table as having quantitative traits.

Usage

create_phe_table_from_ped_table(ped_table)

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.

Value

a single-phenotype tibble, with columns:

• FID the family ID

• IID the within-family ID

• P1 the phenotype

The column names match the PLINK names, see https://www.cog-genomics.org/plink/1.9/input#pheno

Author(s)

Richèl J.C. Bilderbeek

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