cosmetics

common/cp_enrichment.R

@@ -27,7 +27,7 @@ require_auto(DT)
 
 require_auto(clusterProfiler)
 
-devtools::session_info()
+#devtools::session_info() # nice!
 
 ## to fix child support issue with knitr, see also
 ## http://stackoverflow.com/questions/20030523/knitr-nested-child-documents
@@ -180,7 +180,7 @@ cp_test <- function(geneIds){
     goResultsBP <-          enrichGO(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE, ont = "BP") %>% summary()
 
     #cp-bug: if no pathways are enriched odd strucuture is retured ##todo file issue
-    if(!("data.frame" %in% class(keggResults))) keggResults <-filter(goResultsBP, Description="foobar")
+    if(!("data.frame" %in% class(keggResults))) keggResults <- filter(goResultsBP, Description="foobar")
 
     enrResults <- rbind_list(
         mutate(keggResults, ontology="kegg"),
@@ -213,7 +213,7 @@ reload_dplyr()
 ## remove to clumsy gene_id columns
 enrResults %<>% select(-geneID)
 
-write.delim(enrResults, file=paste0(resultsBaseName, "enrResults.txt"))
+write_tsv(enrResults, path=paste0(resultsBaseName, "enrResults.txt"))
 # enrResults <- read.delim(paste0(resultsBaseName, "enrResults.txt"))
 #'  [Enrichment Results](`r paste0(resultsBaseName, "enrResults.txt")`)