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flatironinstitute / inferelator

Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
BSD 2-Clause "Simplified" License
45 stars 12 forks source link

Metadata format #55

Closed poorvam closed 2 years ago

poorvam commented 2 years ago

Hi,

I am using nonbraching metadata (it has 3 columns only) format when running inferelator (https://inferelator.readthedocs.io/en/latest/tutorial.html)

But the program prints below, is there a function to let inferelator use nonbraching format?

Inferelator MPControl using engine multiprocessing Loading expression data file [XXX]_normCounts.tsv Loading metadata file phenotype.tsv Loaded [XXX]_normCounts.tsv: .... .... Skipping metadata because parsing requires missing columns: Index(['del.t', 'isTs', 'prevCol'], dtype='object')

Thanks, Poorva

asistradition commented 2 years ago

If you've created a workflow (e.g. inferer = inferelator_workflow(regression="bbsr", workflow="tfa")), you can set the metadata format with inferer.set_file_properties(metadata_handler='nonbranching').