Commit 87cd7170 authored by Holger Brandl's avatar Holger Brandl

cosmetics

parent 2faeefc3
......@@ -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")`)
......
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