scanpy_plus.pp.assign_sex module

scanpy_plus.pp.assign_sex.assign_sex(data, ygenes=None, use_raw=True, download_gencode=False)

Assigns sex based on XIST and Y-chromosome gene expression.

This function expects log-normalised input. It adds the following columns to adata.obs:

  • XIST_logn: log-normalized expression of XIST

  • Ygene_logn: mean log-normalized expression of the specified Y-chromosome genes

  • XIST_bin: binary indicator for XIST expression

  • Ygene_bin: binary indicator for Y gene expression

  • sex: inferred sex (“male”, “female”, or “ambiguous”)

Parameters:

  • data (anndata.AnnData) – Annotated data matrix.

  • ygenes (list of str or None) – List of Y-chromosome gene names to use. If None: It uses default human chrY list from Ensembl.

  • use_raw (bool, optional) – Whether to use adata.raw values. Defaults to True.

  • download_gencode (bool) – Whether to get chrY genes from gencode and use it. Default False. [Time consuming]

Returns:

Updated AnnData object with sex assignment columns in .obs.

Return type:

anndata.AnnData

Examples

>>> import scanpy as sc
>>> import scanpy_plus as scp
>>> scp.pp.assign_sex(adata, ygenes=['Ddx3y', 'Kdm5d'], use_raw=True)