inote: Integrative Network Omnibus Total Effect Test

In iNOTE: Integrative Network Omnibus Total Effect Test

Description

Omnibus variance-component based testing procedure to test for the total effect of methylation loci and mRNA expression across a network without requiring the specification of an underlying disease risk model.

Usage

inote(iCPG, iGE, iY, iX, i.omniseed=NA, no.pert = 1000, imethod = "chi")

Arguments

iCPG	A list of J CpG matrices with dimensions nxp_{j}.
iGE	An nxJ matrix of gene expression values.
iY	An nx1 dichotomous outcome vector.
iX	An nxr covariate matrix.
i.omniseed	A Jx1 seed vector.
no.pert	No. perturbations per gene level test; defaults to 1000.
imethod	Omnibus testing method – 'chi' or 'uni'

Value

A list with the following components:

p	The omnibus test p-value for the joint, integrative total effect test for the gene set.
p.00	The null distribution of the omnibus test statistic p-value.
method	The omnibus method specified by the user.
gs.uni.mod	If applicable, the omnibus gene-set model selected by the iNOTE-uni method.

Author(s)

Su H. Chu & Yen-Tsung Huang

References

Chu S.H. and Huang Y-T. (2017) Integrative genomic analysis of biological gene sets with applications in lung cancer. (Revise and Resubmit)

Examples

data(X); data(Y); data(CPG); data(GE)
## Not run: inote(iCPG=CPG, iGE=GE, iY=Y, iX=X, no.pert=1000, imethod='chi')

iNOTE documentation built on May 2, 2019, 11:44 a.m.