search_cones {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

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

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.

...

Extra arguments for get_evo_settings.

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

[Package martini version 1.0.0 Index]