Add initial R project file for xMap biomarker analysis

2026-05-12 11:01:52 +02:00
commit 7b124dbe07
29 changed files with 15190 additions and 0 deletions
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+msigdb_workflow <- function(signif.genes, category = "C2") {
+  library(msigdbr)
+  library(ggplot2)
+
+  msigdb_data <- msigdbr(species = "Homo sapiens", category = category)
+  # signif.genes <- reports_P03_Transformed_bcrsn$Set_3_limma
+  # top_genes <- head(signif.genes[order(signif.genes$adj.P.Val),], 25)
+  top_genes <- signif.genes[order(signif.genes$adj.P.Val), ]
+  top_genes <- fill_analyte_info(top_genes)
+  top_genes <- top_genes$Gene.name
+
+  msigdb_genes <- select(msigdb_data, gs_name, gene_symbol)
+  enrich_msigdb <- enricher(top_genes, TERM2GENE = msigdb_genes)
+
+  enrich_msigdb_df <- enrich_msigdb@result %>%
+    separate(BgRatio, into = c("size.term", "size.category"), sep = "/") %>%
+    separate(GeneRatio, into = c("size.overlap.term", "size.overlap.category"), sep = "/") %>%
+    mutate_at(vars("size.term", "size.category", "size.overlap.term", "size.overlap.category"), as.numeric) %>%
+    mutate("k.K" = size.overlap.term / size.term)
+
+  enrich_plot <- enrich_msigdb_df %>%
+    filter(p.adjust <= 0.05) %>%
+    ggplot(aes(x = reorder(Description, k.K), y = k.K)) +
+    geom_col() +
+    theme_classic() +
+    coord_flip() +
+    labs(
+      y = "Significant genes in set / Total genes in set \nk/K", x = "Gene set",
+      title = paste("Differentially expressed genes enriched in", category, "Gene sets (P<0.05)")
+    )
+
+  return(list(data = enrich_msigdb_df, plot = enrich_plot))
+}