cellink.tl.external.run_magma_annotate#

cellink.tl.external.run_magma_annotate(snp_loc, gene_loc, out_prefix, magma_bin='magma', window_kb=0, run=True, **kwargs)#

Run MAGMA Step I — annotate SNPs to genes.

Maps each SNP to the gene(s) whose transcribed region (± window_kb kb) overlaps its position. Creates a .genes.annot file consumed by run_magma_gene_analysis().

Parameters:

snp_loc (str) – Tab-delimited SNP location file with columns SNP, CHR, BP. Can be derived from a GWAS summary statistics file.
gene_loc (str) – NCBI/Ensembl gene location file. MAGMA ships NCBI37.3.gene.loc and NCBI38.gene.loc for GRCh37/38. Format: ENTREZID CHR START END STRAND SYMBOL (tab-delimited, no header).
out_prefix (str) – Prefix for output files. Creates {out_prefix}.genes.annot.
magma_bin (str (default: 'magma')) – Path to the MAGMA binary (default: "magma" assumes it is on PATH).
window_kb (int (default: 0)) – Flanking window in kb added around each gene’s transcribed region (default 0 = gene body only). Use e.g. 35 for ±35 kb.
run (bool (default: True)) – If False, return the command string without executing.
**kwargs – Additional flags passed verbatim to MAGMA as --key value.

Return type:

dict[str, Any]

Returns:

dict annot_file — path to .genes.annot. files_created — list of output paths (if run=True). command — command list (if run=False).

Examples

>>> run_magma_annotate(
...     snp_loc="gwas_snps.txt",
...     gene_loc="NCBI37.3.gene.loc",
...     out_prefix="results/my_gwas",
...     window_kb=35,
... )

cellink.tl.external.run_magma_annotate

Contents

cellink.tl.external.run_magma_annotate#