ind_to_fam: Convert an Eigenstrat IND tibble into a Plink FAM tibble

In genio: Genetics Input/Output Functions

Convert an Eigenstrat IND tibble into a Plink FAM tibble

Description

This function takes an existing IND tibble and creates a FAM tibble with the same information and dummy values for missing data. In particular, the output FAM tibble will contain these columns with these contents (IND only contain id, sex, and label, so there is no loss of information):

• fam: IND label

• id: IND id

• pat: 0 (missing paternal ID)

• mat: 0 (missing maternal ID)

• sex: IND sex converted to Plink integer codes via sex_to_int()

• peno: 0 (missing phenotype)

Usage

ind_to_fam(ind)

Arguments

ind	The input Eigenstrat IND tibble to convert.

Value

A Plink FAM tibble.

See Also

sex_to_int()

Eigenstrat IND format reference: https://github.com/DReichLab/EIG/tree/master/CONVERTF

Plink FAM format reference: https://www.cog-genomics.org/plink/1.9/formats#fam

Examples

# create a sample IND tibble
library(tibble)
ind <- tibble(
  id = 1:3,
  sex = c('U', 'M', 'F'),
  label = c(1, 1, 2)
)
# convert to FAM
fam <- ind_to_fam(ind)
# inspect:
fam

genio documentation built on Jan. 7, 2023, 1:12 a.m.