sigmod.cv_ | R Documentation |
Finds the features maximally associated with a phenotype while being connected in an underlying network. Select the hyperparameters by cross-validation.
sigmod.cv_(X, y, featnames, net)
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. |
A copy of the SnpMatrix$map
data.frame
, with the
following additions:
c: contains the univariate association score for every single SNP.
selected: logical vector indicating if the SNP was selected by SConES or not.
module: integer with the number of the module the SNP belongs to.
X <- as(minigwas[['genotypes']], 'numeric')
X <- X + matrix(rnorm(2500, sd = 0.1), nrow(X), ncol(X))
gi <- get_GI_network(minigwas, snpMapping = minisnpMapping, ppi = minippi)
sigmod.cv_(X, minigwas[['fam']]$affected, minigwas[['map']]$snp, gi)
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