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Supply custom background for enrichment

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This commit is contained in:
Elias Projahn 2022-07-01 12:38:46 +02:00
parent a3164ece43
commit 6db14c4d4a
1 changed files with 11 additions and 5 deletions
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16
R/server.R
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@ -214,10 +214,13 @@ server <- function(options) {
value = 0.0, value = 0.0,
{ # nolint { # nolint
setProgress(0.2) setProgress(0.2)
gprofiler2::gost(results_filtered()[, gene]) gprofiler2::gost(
results_filtered()[, gene],
custom_bg = preset()$gene_ids
)
} }
) )
}) }) |> bindCache(results_filtered(), preset())
output$gost_plot <- plotly::renderPlotly({ output$gost_plot <- plotly::renderPlotly({
gprofiler2::gostplot( gprofiler2::gostplot(
@ -272,11 +275,14 @@ server <- function(options) {
{ # nolint { # nolint
setProgress(0.2) setProgress(0.2)
gene_names <- results_filtered()[, name] all_gene_names <- unique(results()[name != "", name])
gene_names <- unique(gene_names[gene_names != ""]) filtered_gene_names <- unique(results_filtered()[name != "", name])
diseases <- suppressMessages( diseases <- suppressMessages(
disgenet2r::disease_enrichment(gene_names) disgenet2r::disease_enrichment(
all_gene_names,
custom_universe = list(filtered_gene_names)
)
) )
data <- data.table(diseases@qresult) data <- data.table(diseases@qresult)