pertpy.metadata.Drug

pertpy.metadata.Drug#

class Drug[source]#

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#

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

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'], default: 'chembl') – Source of the metadata, chembl, dgidb or pharmgkb.

  • copy (bool, default: False) – Determines whether a copy of the adata is returned.

Return type:

AnnData

Returns:

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

Drug.lookup()[source]#

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.

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