get_genotype: A tools4ukbb function Function output: a dataframe with one...

In Lab-Jaiswal/tools4ukbb: What the Package Does (One Line, Title Case)

A tools4ukbb function Function output: a dataframe with one eid column and one column per variant you select. The variant columns contain the genotypes of each individual. This function, unlike genotypes_df, DOES NOT require a genotype list and, thus, you do not need to know what chromosome your selected variants are located on If the variants you request are not on the chromosomes in your directory, you will get an error

Description

A tools4ukbb function Function output: a dataframe with one eid column and one column per variant you select. The variant columns contain the genotypes of each individual. This function, unlike genotypes_df, DOES NOT require a genotype list and, thus, you do not need to know what chromosome your selected variants are located on If the variants you request are not on the chromosomes in your directory, you will get an error

Usage

get_genotype(variant_df, directory, variants)

Arguments

directory	the directory with your pvar, pgen, and psam files
variants	a list of variants you are interested in
variants_df	dataframe with 3 columns: variant names, their chromosome, and their index. This is generated via

Examples

genotypes_df()

Lab-Jaiswal/tools4ukbb documentation built on May 12, 2022, 9:11 a.m.