scones: Find connected explanatory SNPs.

In martini: GWAS Incorporating Networks

Description

Finds the SNPs maximally associated with a phenotype while being connected in an underlying network (Azencott et al., 2013).

Usage

scones(gwas, net, eta, lambda, score = "chi2", covars = data.frame())

Arguments

gwas	A SnpMatrix object with the GWAS information.
net	An igraph network that connects the SNPs.
eta	Value of the eta parameter.
lambda	Value of the lambda parameter.
score	Association score to measure association between genotype and phenotype. Possible values: chi2 (default), glm.
covars	A data frame with the covariates. It must contain a column 'sample' containing the sample IDs, and an additional columns for each covariate.

Value

A copy of the SnpMatrix$map data.frame, with the following additions:

• c: contains the univariate association score for every single SNP.

• selected: logical vector indicating if the SNP was selected by SConES or not.

• module: integer with the number of the module the SNP belongs to.

References

Azencott, C. A., Grimm, D., Sugiyama, M., Kawahara, Y., & Borgwardt, K. M. (2013). Efficient network-guided multi-locus association mapping with graph cuts. Bioinformatics, 29(13), 171-179. https://doi.org/10.1093/bioinformatics/btt238

Examples

gi <- get_GI_network(minigwas, snpMapping = minisnpMapping, ppi = minippi)
scones(minigwas, gi, 10, 1)

martini documentation built on Nov. 8, 2020, 5:39 p.m.