fix pvalue correction

R/main.R

@@ -104,8 +104,10 @@ cli_run_topgo <- function() {
         name_list <- NULL
     } else {
         input_data <- load_files(cli$genes, cli$background)
-        name_list <- sub(pattern = "(.*)\\..*$",
-                         replacement = "\\1", basename(cli$genes))
+        name_list <- sub(
+            pattern = "(.*)\\..*$",
+            replacement = "\\1", basename(cli$genes)
+        )
     }
     run_topgo(
         input_data, cli$output, cli$id, cli$top, cli$alpha,

R/topGO_analysis.R

@@ -92,8 +92,8 @@ top_go_analysis <- function(de_table, kind, id_kind, go_term_type, regulation,
     df <- as.data.frame(sort(score(results.f)))
     colnames(df) <- c("pvalue")
     df$padj <- p.adjust(df$pvalue, method = "fdr")
-    df$GO.ID <- rownames(head(df, n=top))
-    res <- res %>% left_join(df)
+    df$GO.ID <- rownames(df)
+    res <- res %>% left_join(head(df, n = top))
     return(list(
         res = res, nb_gene = considered_genes, nb_go_gene = nb_go_gene,
         all_go_gene = all_go_gene, all_genes = length(gene_list)