Get_Genotypes_SSD: Get Genotype data from SSD file

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

Get Genotype data from SSD file

Description

Read a SSD file and return a genotype matrix.

Usage

	Get_Genotypes_SSD(SSD_INFO, Set_Index, is_ID = TRUE)
	
	Get_Genotypes_SSD_Sparse(SSD_INFO, Set_Index)
 

Arguments

SSD_INFO	SSD_INFO object returned from Open_SSD.
Set_Index	a numeric value of Set index. The set index of each set can be found from SetInfo object of SSD.INFO.
is_ID	a logical value indicating whether to read SNP ID (default=TRUE). If TRUE, it reads SNP IDs and use them as column names.

Value

A genotype matrix with n rows and m columns, where n is the number of samples and m is the number of SNPs. Get_Genotypes_SSD_Sparse returns a sparse matrix. Get_Genotypes_SSD_Sparse always returns SNP IDs as the column names, so does not have is_ID parameter.

Author(s)

Seunggeun Lee, Larisa Miropolsky

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