scanorama_merge

besca.tl.auto_annot.scanorama_merge(adata_trains, adata_pred, keepdimensionality)

corrects datasets using scanorama and merge training datasets subsequently

This function reads a list of training datasets (at least one) and one testing dataset from .h5ad files and returns a merged and corrected training dataset anndata object, and a corrected testing anndata object.

Parameters:

• adata_trains (list) – list of training dataset adata objects

• adata_pred (AnnData) – testing dataset anndata object

• keepdimensionality (bool) – determines if we should use all common genes or if we should reduce dimensionality to 100. False not currently implemented

• train_datasets (list) – names of train datasets

Returns:

• AnnData – A concatenated and corrected anndata object of all training datasets.

• AnnData – An anndata object containing corrected testing dataset.