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Retrieve input data using biomaRt

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This commit is contained in:
Elias Projahn 2021-09-16 00:06:54 +02:00
parent 040aabc610
commit 1cea6c3631
205 changed files with 187 additions and 3296961 deletions
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46
server.R
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@ -7,45 +7,48 @@ source("process.R")
source("scatter_plot.R")
source("util.R")
# Initialize global static data
# Load input data
inputs <- run_cached("input", load_input, "input")
species <- run_cached("species", retrieve_species)
genes <- run_cached("genes", retrieve_genes)
#' All species excluding species with naturally or artificially short
#' chromosomes.
species_qualified <- inputs$species[median_distance >= 7500000]
distances <- run_cached(
"distances",
retrieve_distances,
species[, id],
genes[, id]
)
#' All known replicatively aging species with long enough chromosomes.
species_replicative <- species_qualified[group == "replicative"]
#' Results computed from [`species_qualified`].
#' Results computed for all species.
results_all <- run_cached(
"results_all",
process_input,
inputs,
species_qualified[, id]
distances,
species[, id],
genes[, id]
)
#' Results computed from [`species_replicative`].
#' Results computed for known replicatively aging species.
results_replicative <- run_cached(
"results_replicative",
process_input,
inputs,
species_replicative[, id]
distances,
species[replicative == TRUE, id],
genes[, id]
)
# Add gene information to results for display.
results_all <- merge(
results_all,
inputs$genes,
genes,
by.x = "gene",
by.y = "id"
)
results_replicative <- merge(
results_replicative,
inputs$genes,
genes,
by.x = "gene",
by.y = "id"
)
@ -95,9 +98,9 @@ server <- function(input, output) {
TPE-OLD genes.",
results[, .N],
results[verified == TRUE, .N],
inputs$genes[verified == TRUE, .N],
genes[verified == TRUE, .N],
results[suggested == TRUE, .N],
inputs$genes[suggested == TRUE, .N]
genes[suggested == TRUE, .N]
)
})
@ -105,13 +108,14 @@ server <- function(input, output) {
results <- results()
gene_ids <- results[input$genes_rows_selected, gene]
genes <- genes[id %chin% gene_ids]
species <- if (input$species == "all") {
species_qualified
species
} else {
species_replicative
species[replicative == TRUE]
}
scatter_plot(gene_ids, inputs, results, species)
scatter_plot(results, species, genes, distances)
})
}