Read_Plink_FAM: Read Plink FAM and covariates files

In SKAT: SNP-Set (Sequence) Kernel Association Test

Read Plink FAM and covariates files

Description

Read Plink FAM and covariates files.

Usage

	Read_Plink_FAM(Filename, Is.binary=TRUE, flag1=0)
	Read_Plink_FAM_Cov(Filename, File_Cov, Is.binary=TRUE, flag1=0, cov_header=TRUE)

 

Arguments

Filename	input file name of plink FAM file
Is.binary	if TRUE, the phenotype is binary. If phenotype is continuous, it should be FALSE
flag1	0 represents the default coding of unaffected/affected (1/2) (default=0), and 1 represents 0/1 coding. flag1=1 is the same as –1 flag in plink. Please see the plink manual.
File_Cov	an input file name of plink covariates file. The first two columns of this file should be FID and IID.
cov_header	a logical value indicating whether the covariate file contains a header row (default=TRUE)

Value

A dataframe of Family ID (FID), Individual ID (IID), Paternal ID (PID), Maternal ID(MID), Sex, and Phenotype. If Read_Plink_FAM_Cov is used with a covariate file, the dataframe has covariates from the 7th column.

Author(s)

Seunggeun Lee

SKAT documentation built on Jan. 15, 2023, 5:10 p.m.