scones_ {martini} | R Documentation

## Find connected explanatory features

### Description

Finds the features maximally associated with a phenotype while being connected in an underlying network.

### Usage

    scones_(X, y, featnames, net, eta, lambda)

### Arguments

`X` | n x d design matrix
`y` | Vector of length n with the outcomes
`featnames` | Vector of length d with the feature names
`net` | An igraph network that connects the SNPs.
`eta` | Value of the eta parameter.
`lambda` | Value of the lambda parameter.

### 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.

### Examples

    X <- as(minigwas[['genotypes']], 'numeric')
    X <- X + matrix(rnorm(2500, sd = 0.1), nrow(X), ncol(X))
    gi <- get_GI_network(minigwas, snpMapping = minisnpMapping, ppi = minippi)
    scones_(X, minigwas[['fam']]$affected, minigwas[['map']]$snp, gi, 10, 1)

[Package martini version 1.14.0 Index]