LGEWIS (version 1.1)

GA.SSD.OneSet_SetIndex: 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()".

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.

%% ~Describe the value returned %% If it is a LIST, use %% \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of 'comp2'} %% ...

Details

Please see SKAT vignettes for using SSD files.