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:

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 1.13.0 Index]