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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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Error: Path '' does not exist train_cell_classifier #39

Closed liliay closed 4 years ago

liliay commented 4 years ago

Hi there, I am actually using Garnett package and i want to train my own classifier. I am running this portion of code as described in the tutorial : library(garnett) library(org.Hs.eg.db) set.seed(260) marker_file_path <- system.file("/cloud-data/eu-ngs/Lilia/garnett-trapnell/extdata/","/cloud-data/eu-ngs/Lilia/garnett-trapnell/hsPBMC_markers.txt", package = "garnett") classifier <- train_cell_classifier(cds = cds_p13, marker_file = marker_file_path, db=org.Hs.eg.db, min_observations = 10, cds_gene_id_type = "ENSEMBL", num_unknown = 50, marker_file_gene_id_type = "ENSEMBL") And the message error I get is : Error: Path '' does not exist

Attached to this request you will find all the informations about my R session. I tried to update the packages but nothing changed. Is there any specific package I need to update ? session_info session_info_2

Thanks in advance to anyone who could guide me to solve this issue.

hpliner commented 4 years ago

This looks like an issue with the path to the marker file. Can you modify the marker_file_path so that it is a simple string path to the file? I.e. "Documents/marker_file.txt"

hpliner commented 4 years ago

I'm going to close due to lack of response, if this is still an issue, please reopen!