GA.SSD.OneSet_SetIndex {LGEWIS}

Genetic association tests for a single region/gene using SSD format files

Description

Test the genetic association between an quantitative outcome and one region/gene using SSD format files.

Usage

GA.SSD.OneSet_SetIndex(SSD.INFO, SetIndex, result.prelim, Gsub.id=NULL,
B=5000, ...)

Arguments

SSD.INFO

SSD format information file, output of function “Open_SSD". The sets are defined by this file.

SetIndex

Set index. From 1 to the total number of sets.

result.prelim

Output of function "GA.prelim()".

Gsub.id

The subject id corresponding to the genotype matrix, an m dimensional vector. This is in order to match the phenotype and genotype matrix. The default is NULL, where the order is assumed to be matched with Y, X, E and time.

B

Number of Bootstrap replicates. The default is 5000.

...

Other options of the generalized score type test. Defined same as in function "GA.test()".

Details

Please see SKAT vignettes for using SSD files.

Value

p.value

P-value of the set based generalized score type test.

p.single

P-values of the incorporated single SNP analyses

n.marker

number of tested SNPs in the SNP set.