Update Enrichr functions

- Implement the option to provide background gene list (Add rba_enrichr_add_background and rewrite other functions accordingly) - Revise function manuals
moosa-r · Dec 26, 2024 · a0866ad · a0866ad
1 parent 04cbeca
commit a0866ad
Show file tree

Hide file tree

Showing 10 changed files with 593 additions and 182 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(rba_connection_test)
 export(rba_enrichr)
+export(rba_enrichr_add_background)
 export(rba_enrichr_add_list)
 export(rba_enrichr_enrich)
 export(rba_enrichr_gene_map)

diff --git a/R/enrichr.R b/R/enrichr.R
diff --git a/R/internal_functions.R b/R/internal_functions.R
@@ -31,13 +31,15 @@
                                               "fly",
                                               "yeast",
                                               "worm",
-                                              "fish")),
+                                              "fish",
+                                              "speedrichr")),
                                   human = "Enrichr/",
                                   fly = "FlyEnrichr/",
                                   yeast = "YeastEnrichr/",
                                   worm = "WormEnrichr/",
-                                  fish = "FishEnrichr/"),
-                     ptn = "^(https?://)?(www\\.)?maayanlab\\.cloud/.*Enrichr/",
+                                  fish = "FishEnrichr/",
+                                  speedrichr = "speedrichr/api/"),
+                     ptn = "^(https?://)?(www\\.)?maayanlab\\.cloud/(.*Enrichr|speedrichr)/",
                      err_ptn = "^$"
                    ),
                    ensembl = switch(

diff --git a/man/rba_enrichr.Rd b/man/rba_enrichr.Rd
diff --git a/man/rba_enrichr_add_background.Rd b/man/rba_enrichr_add_background.Rd
diff --git a/man/rba_enrichr_add_list.Rd b/man/rba_enrichr_add_list.Rd
diff --git a/man/rba_enrichr_enrich.Rd b/man/rba_enrichr_enrich.Rd