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Add framework for progress information

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This commit is contained in:
Elias Projahn 2021-10-19 15:03:10 +02:00
parent 16e83d38a8
commit 37f468658c
6 changed files with 76 additions and 11 deletions
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14
R/correlation.R
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@ -1,6 +1,6 @@
# Compute the mean correlation coefficient comparing gene distances with a set
# of reference genes.
correlation <- function(distances, preset) {
correlation <- function(distances, preset, progress = NULL) {
results <- data.table(gene = preset$gene_ids)
reference_gene_ids <- preset$reference_gene_ids
reference_count <- length(reference_gene_ids)
@ -14,6 +14,9 @@ correlation <- function(distances, preset) {
# Prepare the reference genes' data.
reference_distances <- distances[gene %chin% reference_gene_ids]
genes_done <- 0
genes_total <- length(preset$gene_ids)
# Perform the correlation for one gene.
compute <- function(gene_id) {
gene_distances <- distances[gene_id]
@ -29,7 +32,7 @@ correlation <- function(distances, preset) {
# Correlate with all reference genes but not with the gene itself.
for (reference_gene_id in
reference_gene_ids[reference_gene_ids != gene_id]) {
reference_gene_ids[reference_gene_ids != gene_id]) {
data <- merge(
gene_distances,
reference_distances[reference_gene_id],
@ -55,6 +58,13 @@ correlation <- function(distances, preset) {
# Compute the score as the mean correlation coefficient.
score <- correlation_sum / reference_count
if (!is.null(progress)) {
genes_done <<- genes_done + 1
progress(genes_done / genes_total)
}
score
}
results[, score := compute(gene), by = 1:nrow(results)]