Has anyone ever run through this tutorial?
I'm getting some error messages when I try and run this. The first error is in this command:
IDs <- select(project_catalog, Sequence.Read.Archive.ID, HMP.Isolation.Body.Site, Gene.Count) %>% filter(HMP.Isolation.Body.Site=='gastrointestinal_tract' & Gene.Count>0) %>% .$Sequence.Read.Archive.ID length(IDs)
The error message is "unexpected symbol in IDs". It will run Ok if I delete the last %>% and everything following, but I'm afraid deleting that portion is causing errors in the next command :
tsvs<-lapply(IDs, function(x) read.csv(file.path(PATH,paste0(x,'.tsv')),sep='\t') %>% transmute(Reference.Name=Reference.Name,Nreads=DepthBreadthTotal.reference.bases/10000))
That throws an error of "Error in file(file, "rt") : invalid 'description' argument