run_GBA: Performing 'Guilt by Association' Analysis

Description Usage Arguments Value Examples

View source: R/run_GBA.R

Description

The function runs and evaluates gene function prediction based on the 'guilt by association'-principle using neighbor voting (neighbor_voting) [1]. As a measure of performance and significance of results, AUCs of all evaluated functional groups are calculated.

Usage

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run_GBA(network, labels, min = 20, max = 1000, nfold = 3)

Arguments

network

numeric array symmetric, gene-by-gene matrix

labels

numeric array

min

numeric value to limit gene function size

max

numeric value to limit gene function size

nfold

numeric value, default is 3

Value

list roc.sub, genes, auroc

Examples

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genes.labels <- matrix( sample( c(0,1), 1000, replace=TRUE), nrow=100)
rownames(genes.labels) = paste('gene', 1:100, sep='')
colnames(genes.labels) = paste('function', 1:10, sep='')
net <- cor( matrix( rnorm(10000), ncol=100), method='spearman')
rownames(net) <- paste('gene', 1:100, sep='')
colnames(net) <- paste('gene', 1:100, sep='')

gba <- run_GBA(net, genes.labels, min=10) 

sarbal/EGAD documentation built on Aug. 1, 2018, 1:38 a.m.