Get_Genotypes_SSD

Get_Genotypes_SSD_Sparse

Read a SSD file and return a genotype matrix.

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

Get_Genotypes_SSD function

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

Arguments

Author

Get Genotype data from SSD file — Get_Genotypes_SSD

<dl>

 <dt>SSD_INFO</dt>
<dd>SSD_INFO object returned from Open_SSD.</dd>

 <dt>Set_Index</dt>
<dd>a numeric value of Set index. The set index of each set can be found from SetInfo object of SSD.INFO.</dd>

 <dt>is_ID</dt>
<dd>a logical value indicating whether to read SNP ID (default=TRUE). If TRUE, it reads SNP IDs and use them as column names.</dd>

</dl>

Get_Genotypes_SSD: Get Genotype data from SSD file

Description

Usage

Value

Arguments

Author