ukbtools (version 0.11.3)

ukb_gen_het: Heterozygosity outliers

Description

Defunct. See help("ukb_defunct").

Heterozygosity outliers are typically removed from genetic association analyses. This function returns either a vector of heterozygosity outliers to remove (+/- 3sd from mean heterozygosity), or a data frame with heterozygosity scores for all samples.

Usage

ukb_gen_het(data, all.het = FALSE)

Arguments

data

A UKB dataset created with ukb_df.

all.het

Set all.het = TRUE for heterozygosity scores for all samples. By default all.het = FALSE returns a vector of sample IDs for individuals +/-3SD from the mean heterozygosity.

Value

A vector of IDs if all.het = FALSE (default), or a dataframe with ID, heterozygosity and PCA-corrected heterozygosity if all.het = TRUE.

Details

UKB have published full details of genotyping and quality control for the interim genotype data.

Examples

# NOT RUN {
#' # Heterozygosity outliers (+/-3SD)
outlier_het_ids <- ukb_gen_het(my_ukb_data)

# Retrieve all raw and pca-corrected heterozygosity scores
ukb_het <- ukb_gen_het(my_ukb_data, all.het = TRUE)
# }