cellink.tl.external.genesets_dir_to_entrez_gmt

cellink.tl.external.genesets_dir_to_entrez_gmt(*, geneset_dir='ldsc_genesets', out_gmt=None, ensembl_to_entrez_tsv=None, pattern='*.GeneSet', description='S-LDSC derived gene set (Entrez)', include_control=False, control_name='Control', remove_version_suffix=True, uppercase=True, min_genes=1, sort_genes=False, dedup_genes=True, drop_unmapped=True, allow_mygene_fallback=False, species='human', output_basename='genesets.gmt')

Return type:

Path

Convert *.GeneSet (Ensembl IDs) -> MAGMA .gmt with Entrez IDs.

Defaults:

• reads from ./ldsc_genesets

• writes to a sibling directory ./magma_genesets/genesets.gmt (magma_genesets is created if needed)

Preferred: provide ensembl_to_entrez_tsv for offline mapping. Optional: allow_mygene_fallback=True to query mygene.info (needs internet).