longskat_get_gene: Get SNP matrix of gene.

In ZWang-Lab/LSKAT: SNP-set (Sequence) Kernel Association Test for longitudinal data.

Description

This function provides a interface to read all SNPs of genes from the PLINK data object.

Usage

longskat_get_gene(  gen.obj, gene.set, snp.impute="mean", verbose = FALSE )

Arguments

gen.obj	Reference class , it is a wrapper of plink data object obtained from the function longskat_plink_load.
gene.set	Vector of numeric or string, indicating the gene index or gene name.
snp.impute	String, indicating the method of SNP imputation, the default model uses the mean of each variant to replace the missing SNP data. Two optional values: 'mean' or 'random'.
verbose	Logical variable, indicating whether some debug information can be outputted.

;

Details

The parameter gene.set can be gene index (numeric) or gene names (string).

Value

The returned list object could contain multiple genes. It includes

snp.mat	List, SNP Matrices for genes in gene.set.
maf	List, SNP MAF vectors for genes in gene.set.
nmiss	List, SNP missing information for genes in gene.set.
gene.name	List, gene names for genes in gene.set.

References

Wang Z., Xu K., Zhang X., Wu X., and Wang Z., (2016) Longitudinal SNP-set association analysis of quantitative phenotypes. Genetic Epidemiology.

See Also

longskat_plink_load and longskat_gene_test

Examples

## data simulation for the power test
p0 <- longskat_gene_simulate( plink.format=T, file.plink.prefix="tmp-plink-load", 
      power.test=T, n.gene=20);

## Loading PLINK data set into the reference object
plk <- longskat_plink_load ( p0$file.plink.bed, p0$file.plink.bim, p0$file.plink.fam, 
      p0$file.gene.set,  verbose=TRUE);

## Retriving the SNP matrix from the reference object
snps <- longskat_get_gene( plk, 1:2, snp.impute="mean" );

## show the structures of the result.
str(snps);

ZWang-Lab/LSKAT documentation built on May 10, 2019, 1:55 a.m.