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Fix bugs in correlation method

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This commit is contained in:
Elias Projahn 2021-10-19 17:34:36 +02:00
parent 37f468658c
commit e6bca4d515
1 changed files with 12 additions and 4 deletions
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16
R/correlation.R
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@ -31,8 +31,11 @@ correlation <- function(distances, preset, progress = NULL) {
correlation_sum <- 0 correlation_sum <- 0
# Correlate with all reference genes but not with the gene itself. # Correlate with all reference genes but not with the gene itself.
for (reference_gene_id in gene_reference_gene_ids <- reference_gene_ids[
reference_gene_ids[reference_gene_ids != gene_id]) { reference_gene_ids != gene_id
]
for (reference_gene_id in gene_reference_gene_ids) {
data <- merge( data <- merge(
gene_distances, gene_distances,
reference_distances[reference_gene_id], reference_distances[reference_gene_id],
@ -50,14 +53,19 @@ correlation <- function(distances, preset, progress = NULL) {
# relation. # relation.
setorder(data, distance.y) setorder(data, distance.y)
correlation_sum <- correlation_sum + abs(stats::cor( correlation <- abs(stats::cor(
data[, distance.x], data[, distance.y], data[, distance.x], data[, distance.y],
method = "spearman" method = "spearman"
)) ))
# If the correlation is NA, this will effectively mean 0.0.
if (!is.na(correlation)) {
correlation_sum <- correlation_sum + correlation
}
} }
# Compute the score as the mean correlation coefficient. # Compute the score as the mean correlation coefficient.
score <- correlation_sum / reference_count score <- correlation_sum / length(gene_reference_gene_ids)
if (!is.null(progress)) { if (!is.null(progress)) {
genes_done <<- genes_done + 1 genes_done <<- genes_done + 1