longskat_snp_plink: Single SNP associaion test using LSKAT for 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_snp_plink(file.plink.bed, 
    file.plink.bim, 
    file.plink.fam,
    file.phe.long, 
    file.phe.cov,
    file.phe.time = NULL, 
    file.gene.set=NULL,
    snp.set = NULL, 
    options = list(),
    verbose=FALSE);

Arguments

file.plink.bed	File name, PLINK bed file
file.plink.bim	File name, PLINK bim file
file.plink.fam	File name, PLINK fam file
file.phe.long	File name, indicating phenotype file in CSV format with row name (individual ID) and header information (Measured Index). Each individual is encoded to one row data which has individual ID as row name and multiple observed values followed by row name.
file.phe.cov	File name, indicating covariate file in CSV format with row name (individual ID) and header information (Covariate Index). Each individual is encoded to one row data which has individual ID as row name and covariate values followed by row name.
file.phe.time	File name, indicating measured times in CSV format with row name (individual ID) and header information (Measured Time). Each individual is encoded to one row data which has individual ID as row name and covariate values followed by row name.
file.gene.set	File name, indicating gene set table which has two columns, 1st column is gene name, 2nd column is variant name and no header.
snp.set	numeric or string. indicating the gene name or gene index in the gene set table
options	String, see the details
verbose	Logical variable, indicating whether some debug information can be outputted.

Details

None

Value

A list object with 3 items is returned by this function:

par	The parameters of this function call.
mle	The estimation of NULL Model returned by longskat_est_model, including model parameters and residuals, please refer to the structure in longskat_est_model.
result	Matrix containing the test result of LSKAT for all SNPs, the sub-items are described as follows.

The structure: of result item:

index	Number, gene index
snp.name	String, snp name
gene.name	String, gene name
chr	Number, chromosome
pos	Number, position
MAF	Number, Minor Allel Frequency.
NMISS	Number, number of missing SNP.
rare	Logical, rare SNP or not.
q.lskat	Numeric, the statistical test of LSKAT
p.lskat	Numeric, the p-value of LSKAT

Examples

## data simulation for the power test.
p1 <- longskat_gene_simulate( plink.format=T, file.plink.prefix="tmp-simu-snp", 
      power.test=T, n.gene=2);

## Single SNP test by LSKAT 
r.lskat <- longskat_snp_plink( p1$file.plink.bed, p1$file.plink.bim, p1$file.plink.fam, 
      p1$file.phe.long, p1$file.phe.cov, NULL, p1$file.gene.set );

## show the result
print(r.lskat);

## draw the result in the Manhattan figure.
plot(r.lskat, "tmp-simu-snp.pdf", "title")

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