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", 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")

[Package martini version 1.6.0 Index]