mantispy.io.unexpressed_genes

mantispy.io.unexpressed_genes#

mantispy.io.unexpressed_genes(expression, cell_line, *, tpm_cutoff=0.0)[source]#

Gene symbols a cell line does not express, read from DepMap as an empirical null for hit calling.

The reference is always a DepMap expression matrix you have downloaded, so the null is tied to the screened cell line rather than to any hard-coded reference. Nothing is downloaded or re-hosted; point it at the file from the DepMap data page, such as OmicsExpressionProteinCodingGenesTPMLogp1.csv (one row per model, gene columns named "SYMBOL (ENTREZ)", holding log2(TPM+1)). The cell line is named by its DepMap model id, DepMap’s own key, so the lookup reuses their identifier directly. A gene is unexpressed when its value is at or below tpm_cutoff, which is zero for the zero-TPM genes PERISCOPE uses.

Parameters:

  • expression (str | Path | DataFrame) – A DepMap expression matrix, as a path or a loaded frame indexed by model id.

  • cell_line (str) – The DepMap model id to read, such as "ACH-000364" for U2OS.

  • tpm_cutoff (float (default: 0.0)) – The log2(TPM+1) value at or below which a gene is called unexpressed.

Return type:

set[str]

Returns:

The set of unexpressed gene symbols.

Raises:

ValueError – cell_line is not a row of the expression matrix.