Merge pull request #107 from bcbio/fix_65

Fix 65

Author: lpantano

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: person("Pantano", "Lorena", , "lorena.pantano@gmail.com",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.

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
 
 }

…1_quality_assessment/params_qc-example.R …plates/rnaseq/00_params/params-example.Rinst/templates/rnaseq/01_quality_assessment/params_qc-example.R renamed to inst/templates/rnaseq/00_params/params-example.R inst/templates/rnaseq/01_quality_assessment/params_qc-example.R renamed to inst/templates/rnaseq/00_params/params-example.R

@@ -1,5 +1,6 @@
-# info params
-
+# project params
+date = "YYYYMMDD"
+basedir <- './' # where to write down output files
 
 # Example data
 coldata_fn='https://raw.githubusercontent.com/bcbio/bcbioR-test-data/devel/rnaseq/nf-core/coldata.csv'

…rnaseq/01_quality_assessment/params_qc.R inst/templates/rnaseq/00_params/params.Rinst/templates/rnaseq/01_quality_assessment/params_qc.R renamed to inst/templates/rnaseq/00_params/params.R inst/templates/rnaseq/01_quality_assessment/params_qc.R renamed to inst/templates/rnaseq/00_params/params.R

@@ -1,4 +1,6 @@
 # info params
+date = "YYYYMMDD"
+basedir <- './' # where to write down output files
 
 # Your data
 # This is the file used to run nf-core or compatible to that

inst/templates/rnaseq/01_quality_assessment/QC.Rmd

@@ -17,8 +17,8 @@ output:
 params:
   # Fill this file with the right paths to nfcore output
   # Put hg38, mm10, mm39, or other
-  # params_file: params_qc-example.R # example data
-  params_file: params_qc-example.R
+  # params_file: ../00_params/params.R 
+  params_file: ../00_params/params-example.R # example data
   genome: hg38
   single_end: false
   factor_of_interest: sample_type

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

@@ -25,7 +25,8 @@ params:
   genome: hg38
   ruv: false
   combatseq: false
-  params_file: params_de-example.R
+  # params_file: ../00_params/params.R 
+  params_file: ../00_params/params-example.R
   project_file: ../information.R
   functions_file: ../00_libs
 ---
@@ -659,7 +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