This function writes a space-delimited file with header, with the obligatory first two columns FID and IID. Use this function to write phenotype and covariate files for downstream genetic analysis in plink - the format is the same.
ukb_gen_write_plink(x, path, ukb.variables, ukb.id = "eid", na.strings = "NA")A UKB dataset.
A path to a file.
A character vector of either the phenotypes for a PLINK phenotype file, or covariates for a PLINK covariate file.
The id variable name (default = "eid").
String used for missing values. Defaults to NA.
The function writes the id variable in your dataset to the first two columns of the output file with the names FID and IID - you do not need to have two id columns in the data.frame passed to the argument x. Use the --pheno-name and --covar-name PLINK flags to select columns by name. See the PLINK documentation for the --pheno, --mpheno, --pheno-name, and --covar, --covar-name, --covar-number flags.
ukb_gen_read_sample to read a sample file, and ukb_gen_write_bgenie to write phenotype and covariate files to BGENIE format.
if (FALSE) {
# Automatically inserts FID IID columns required by PLINK
ukb_gen_write_plink(
my_ukb_data,
path = "my_ukb_plink.pheno",
ukb.variables = c("height", "weight", "iq")
)
ukb_gen_write_plink(
my_ukb_data,
path = "my_ukb_plink.cov",
ukb.variables = c("age", "socioeconomic_status", "genetic_pcs")
)
}