read_data

besca.tl.auto_annot.read_data(train_paths, train_datasets, test_path, test_dataset, use_raw=False)

Function to read in training and testing datasets

This function reads a list of training datasets (at least one) and one testing dataset, either from raw or processed. It returns a list of training dataset adata object, and the testing adata object.

Parameters:

• train_paths (list) – list of paths where training datasets are located

• train_datasets (list) – a list of names of training datasets (same order as paths)

• test_path (string) – path of test dataset

• test_dataset (string) – name of test dataset

• use_raw (bool | default = False) – whether to use processed adata object or cp10k normalized counts

Returns:

• list – lits of training anndata objects.

• AnnData – Anndata object with testing dataset

• AnnData – test dataset anndata object that will not be modified, is used to append prediction column to.