pertpy.metadata.Drug

class pertpy.metadata.Drug

Utilities to fetch metadata for drug studies.

Methods table

annotate(adata[, source, copy])	Annotates genes by their involvement in applied drugs.
lookup()	Generate LookUp object for Drug.

Methods

annotate

Drug.annotate(adata, source='chembl', copy=False)

Annotates genes by their involvement in applied drugs.

Genes need to be in HGNC format.

Parameters:

• adata (AnnData) – AnnData object containing log-normalised data.

• source (Literal['chembl', 'dgidb', 'pharmgkb']) – Source of the metadata, chembl, dgidb or pharmgkb. Defaults to chembl.

• copy (bool) – Determines whether a copy of the adata is returned. Defaults to False.

Return type:

AnnData

Returns:

An AnnData object with a new column drug in the var slot.

lookup

Drug.lookup()

Generate LookUp object for Drug.

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

Return type:

LookUp

Returns:

Returns a LookUp object specific for drug annotation.