scones {martini}R Documentation

Find connected explanatory SNPs.

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:

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)

[Package martini version 1.10.0 Index]