preprocess_genedata: preprocess_genedata

In ZIM4rv: Gene‐based Association Tests of Zero‐inflated Count Phenotype for Rare Variants

preprocess_genedata

Description

Preprocess genotype files in PLINK format

This function converts PLINK format files into data frames containing genotypes information in proper format for the model fitting and testing.

Usage

preprocess_genedata(fam_file, dosage_file, region_file, gene_name)

Arguments

fam_file	.fam file in PLINK format
dosage_file	a dosage file includes dosage information of each variant for all individuals
region_file	a file listing genetic regions where each row contains chromosome, basepairs and the name of genetic region respectively
gene_name	a character string of the name of a gene, e.g."CEPT". The name is case-sensitive.

Value

a data frame containing genotypes for all individuals in the required format for model fitting and testing

Examples

data(Ex2_fam)
data(Ex2_dosage)
data(Ex2_region)
preprocess_genedata(Ex2_fam,Ex2_dosage,Ex2_region,"r2")

ZIM4rv documentation built on April 3, 2025, 7:39 p.m.