dropFeatures
Short Description
sm.hl.dropFeatures
: A handy function that allows users to susbet the anndata object.
The function can be used to drop markers, cells, columns in metadata, groups of cells belonging to a certain category.
Function
dropFeatures(adata, drop_markers=None, drop_cells=None, drop_meta_columns=None, drop_groups=None, groups_column=None, subset_raw=True)
Parameters
adata : AnnData Object
drop_markers (list):
Provide a list of markers to drop. The default is None.
drop_cells (list):
Provide a list of cells (index name) to drop. The default is None.
drop_meta_columns (list):
Provide a list of column names in `adata.obs` to drop. The default is None.
drop_groups (list):
Provide a list of categorical names to drop.
Works in conjunction with `groups_column`. The default is None.
groups_column (str):
Pass the column name of the column that contains the categories passed to
`drop_groups`. The default is None.
subset_raw (bool):
Generally any subsetting of `AnnData` object does not affect the raw data
stored in `adata.raw`. Pass `True` to apply the same transformations to
`adata.raw` as well. The default is True.
Returns
adata : Modified `adata` object
Example
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Source code in scimap/helpers/_dropFeatures.py
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