longskat_plink_load: Loading plink data set.

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

Description

This function provides a pipeline for the plink data set based on the LSKAT function. Except the plink data set(BED, BIM and FAM), SNP set table is same as SKAT package.

Usage

longskat_plink_load(file.plink.bed, 
    file.plink.bim, 
    file.plink.fam,
    file.gene.set,
    plink.path=NULL,
    verbose=FALSE)

Arguments

file.plink.bed	File name, PLINK bed file, containing the packed binary SNP genotype data
file.plink.bim	File name, PLINK bim file, containing the SNP descriptions
file.plink.fam	File name, PLINK fam file, containing subject(and, possibly, family) identifiers
file.gene.set	File name, indicating SNP set table which has two columns, gene name in 1st column and variant name in 2nd column and no header.
plink.path	String, indicating PLINK command path, for the large PLINK data, the package will load partial plink data extracted by the plink command rather than the whole data set.
verbose	Logical Variable, indicating whether some information are outputted for debug.

Details

The SNP set file is same as the SetID file in SKAT package which is white-space (space or tab) seperated file with 2 columns: SetID (1st column) and SNP_ID (2nd column), Please keep in mind that there should be no header!

Value

This function returns a reference class ("'PLINK.refer'")for PLINK data operation which provides a interface to access the SNP information. longskat_get_gene use this object to extract the SNP matrix for genes.

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_get_gene

Examples

## see the example in the function longskat_get_gene

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