ukb_gen_write_plink_excl: Writes a PLINK format file for combined exclusions

In ukbtools: Manipulate and Explore UK Biobank Data

Description

Defunct. See help("ukb_defunct"). Writes a combined exclusions file including UKB recommended exclusions, heterozygosity exclusions (+/- 3*sd from mean), genetic ethnicity exclusions (based on the UKB genetic ethnic grouping variable, field 1002), and relatedness exclusions (a randomly-selected member of each related pair). For exclusion of individuals from a genetic analysis, the PLINK flag --remove accepts a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column (i.e., FID IID), without a header.

Usage

ukb_gen_write_plink_excl(path)

Arguments

path	A path to a file.

See Also

ukb_gen_meta, ukb_gen_pcs which retrieve variables to be included in a covariate file. ukb_gen_excl_to_na to update a phenotype with NAs for samples to-be-excluded based on genetic metadata, and ukb_gen_write_plink and ukb_gen_write_bgenie

Examples

## Not run: 
# Supply name of a file to write PLINK format combined exclusions
ukb_gen_write_plink_excl("combined_exclusions.txt")

## End(Not run)

ukbtools documentation built on May 15, 2019, 5:04 p.m.