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Create a multi-assay experiment from PathoScope 2.0 output for usage with animalcules

Source: R/convert_animalcules_patho.R
convert_animalcules_patho.Rd

This function serves as a legacy integration method for usage with PathoScope 2.0 outputs. Upon completion of the PathoScope 2.0 pipeline, users can analyze and visualize abundances in their samples using the animalcules package. After running this function, the user should save the returned MAE to an RDS file using a function like saveRDS to upload the output into the animalcules package.

Usage

convert_animalcules_patho(
  patho_counts,
  annot_path,
  which_annot_col,
  end_string = "-sam-report.tsv"
)

Arguments

patho_counts

Character string, a directory filepath to the counts ID CSVs output by metascope_id().

annot_path

The filepath to the CSV annotation file for the samples.

which_annot_col

The name of the column of the annotation file containing the sample IDs. These should be the same as the meta_counts root filenames.

end_string

The end string used at the end of the metascope_id files. Default is ".metascope_id.csv".

Value

Returns a MultiAssay Experiment file of combined sample counts data. The MultiAssay Experiment will have a counts assay ("MGX").