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Set network diagonal to zeros to prevent using the known data of each gene on their own prediction. #7

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Set network diagonal to zeros to prevent using the known data of each gene on their own prediction. #7

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7 changes: 2 additions & 5 deletions R/predictions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,8 @@ predictions <- function(genes.labels, network) {
network <- network[filt.net, filt.net]
genes.labels <- as.matrix(genes.labels[filt.lab, ])

# genes.label : needs to be in 1s and 0s
l <- dim(genes.labels)[2]
g <- dim(genes.labels)[1]
ab <- which(genes.labels != 0, arr.ind = TRUE)
n <- length(ab[, 1])
# Make sure the network diagonal (geneA vs geneA, geneB vs geneB, etc) is set to zero, else the predictions for a gene would be boosted by the already known data on it, messing the F1 score.
diag(network) <- 0

# Get sums - mat. mul.
sumin <- (t(network) %*% genes.labels)
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