cellink.tl.external.scores_to_gmt#

cellink.tl.external.scores_to_gmt(scores, out_file, top_frac=0.1, ascending=False, gene_map=None, set_name_prefix='', min_genes=1)#

Convert a genes × cell-types score DataFrame to MAGMA GMT format.

Each cell type becomes one gene set containing the top (or bottom) top_frac fraction of genes ranked by score. This is the Python-API equivalent of make_magma_gmt.py in the combined_pipeline.

GMT format: set_name\\tNA\\tGENE1\\tGENE2\\t... (one line per set).

Parameters:

scores (DataFrame) – DataFrame with genes as rows and cell types as columns. Index should contain gene identifiers (ENSG IDs or gene symbols).
out_file (str | Path) – Output .gmt file path.
top_frac (float (default: 0.1)) – Fraction of genes to select per cell type (default 0.10 = top 10%).
ascending (bool (default: False)) – If True, select the bottom top_frac genes (lowest scores) instead of the top.
gene_map (str | Path | Series | None (default: None)) –
Optional mapping from gene symbols to ENSG IDs. Accepts:
- str or Path — path to a two-column TSV with headers gene_name and ensg_id.
- pd.Series — index = gene symbol, values = ENSG ID.
If provided, non-ENSG index entries are translated and rows that still do not look like ENSG IDs after mapping are dropped.
set_name_prefix (str (default: '')) – String prepended to every set name (e.g. "brainscope_scz_seismic_top").
min_genes (int (default: 1)) – Minimum number of genes required to write a gene set. Sets with fewer genes are skipped with a warning.

Return type:

Path

Returns:

Path Path to the written GMT file.

Examples

>>> from cellink.tl.external import scores_to_gmt, run_magma_gsa
>>> gmt = scores_to_gmt(specificity_df, "ExcL23_top10.gmt", set_name_prefix="brainscope_seismic_top")
>>> run_magma_gsa(gene_results="scz.genes.raw", set_annot=str(gmt), out_prefix="results/scz_gsa")

cellink.tl.external.scores_to_gmt

Contents

cellink.tl.external.scores_to_gmt#