fix FA function

Author: lpantano

inst/templates/rnaseq/00_libs/FA.R

@@ -40,15 +40,15 @@ get_databases=function(sps="human"){
 }
 
 run_fora_v2=function(input, uni, all_in_life){
-  total_deg=length(unique(input$ENTREZID))/length(unique(uni$ENTREZID))
+  total_deg=length(unique(input$entrez))/length(unique(uni$entrez))
   pathways_ora_all = lapply(names(all_in_life), function(database){
     p = all_in_life[[database]]
     #browser()
     pathway = split(x = p$entrez_gene, f = p$gs_name)
     db_name = database
     respath <- fora(pathways = pathway,
-                    genes = unique(input$ENTREZID),
-                    universe = unique(uni$ENTREZID),
+                    genes = unique(input$entrez),
+                    universe = unique(uni$entrez),
                     minSize  = 15,
                     maxSize  = 500)
     respath  %>%
@@ -57,11 +57,11 @@ run_fora_v2=function(input, uni, all_in_life){
     mutate(analysis="ORA")
   ora_tb = pathways_ora_all %>% unnest(overlapGenes) %>%
     group_by(pathway) %>%
-    left_join(uni, by =c("overlapGenes"="ENTREZID")) %>%
-    dplyr::select(pathway, padj, NES, SYMBOL, analysis,
+    left_join(uni, by =c("overlapGenes"="entrez")) %>%
+    dplyr::select(pathway, padj, NES, gene_name, analysis,
                   database) %>%
     group_by(pathway,padj,NES,database,analysis) %>%
-    summarise(genes=paste(SYMBOL,collapse = ","))
+    summarise(genes=paste(gene_name,collapse = ","))
   ora_tb
 
 }

inst/templates/rnaseq/02_differential_expression/DEG.Rmd

@@ -660,7 +660,7 @@ fa_list=lapply(de_list,function(contrast){
   #change to the right species
   input_entrezid <- rdata %>% filter(gene_id %in% ora_input, !is.na(entrez))
     # AnnotationDbi::select(ann.org, ora_input, 'ENSEMBL', columns = c('ENTREZID', 'SYMBOL'))
-  all=run_fora_v2(input_entrezid, universe_mapping,all_in_life)
+  all=run_fora_v2(input_entrezid, universe_mapping, all_in_life)
   
   ora_input = res %>% filter(!is.na(padj), padj<0.01, lfc> 0.3) %>% pull(gene_id)
   #change to the right species