Read_Plink_FAM

Read_Plink_FAM_Cov

Read Plink FAM and covariates files.

Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.

Seunggeun Lee

SKAT

SNP-Set (Sequence) Kernel Association Test

Read_Plink_FAM function

<dl> <dt>Filename</dt>
<dd>input file name of plink FAM file</dd> <dt>Is.binary</dt>
<dd>if TRUE, the phenotype is binary. If phenotype is continuous, it should be FALSE</dd> <dt>flag1</dt>
<dd>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.</dd>
 
	 <dt>File_Cov</dt>
<dd>an input file name of plink covariates file. The first two columns of this file should be FID and IID.</dd>
 
	 <dt>cov_header</dt>
<dd>a logical value indicating whether the covariate file contains a header row (default=TRUE)</dd>
 
	
</dl>

Arguments

Author

Read Plink FAM and covariates files — Read_Plink_FAM

<dl>

 <dt>Filename</dt>
<dd>input file name of plink FAM file</dd>

 <dt>Is.binary</dt>
<dd>if TRUE, the phenotype is binary. If phenotype is continuous, it should be FALSE</dd>

 <dt>flag1</dt>
<dd>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.</dd>
 
	 <dt>File_Cov</dt>
<dd>an input file name of plink covariates file. The first two columns of this file should be FID and IID.</dd>
 
	 <dt>cov_header</dt>
<dd>a logical value indicating whether the covariate file contains a header row (default=TRUE)</dd>
 
	
</dl>

Read_Plink_FAM: Read Plink FAM and covariates files

Description

Usage

Value

Arguments

Author