pertpy.metadata.Moa¶

class pertpy.metadata.Moa[source]¶: Utilities to fetch metadata for mechanism of action studies.

Methods table¶

`annotate`(adata[, query_id, target, ...])	Annotate cells affected by perturbations by mechanism of action.
`lookup`()	Generate LookUp object for Moa metadata.

Methods¶

annotate¶

Moa.annotate(adata, query_id='perturbation', target=None, verbosity=5, copy=False)[source]¶

Annotate cells affected by perturbations by mechanism of action.

For each cell, we fetch the mechanism of action and molecular targets of the compounds sourced from clue.io.

Parameters:

adata (AnnData) – The data object to annotate.
query_id (str) – The column of .obs with the name of a perturbagen. Defaults to ‘perturbation’.
target (str | None) – The column of .obs with target information. If set to None, all MoAs are retrieved without comparing molecular targets. Defaults to None.
verbosity (int | str) – The number of unmatched identifiers to print, can be either non-negative values or ‘all’. Defaults to 5.
copy (bool) – Determines whether a copy of the adata is returned. Defaults to False.

Return type:

AnnData

Returns:

Returns an AnnData object with MoA annotation.

lookup¶

Moa.lookup()[source]¶

Generate LookUp object for Moa metadata.

The LookUp object provides an overview of the metadata to annotate. annotate_moa function has a corresponding lookup function in the LookUp object, where users can search the query_ids and targets in the metadata.

Return type:: LookUp
Returns:: Returns a LookUp object specific for MoA annotation.