search_cones: 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

search_cones(gwas, net, encoding = "additive", sigmod = FALSE, ...)

Arguments

gwas	A SnpMatrix object with the GWAS information.
net	An igraph network that connects the SNPs.
encoding	SNP encoding. Possible values: additive (default), resessive, dominant, codominant.
sigmod	Boolean. If TRUE, use the Sigmod variant of SConES, meant to prioritize tightly connected clusters of SNPs.
...	Extra arguments for get_evo_settings.

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)
search_cones(minigwas, gi)
search_cones(minigwas, gi, encoding = "recessive")
search_cones(minigwas, gi, associationScore = "skat")

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