cellink.tl.external.run_magma_gene_analysis

cellink.tl.external.run_magma_gene_analysis(bfile, pval_file, gene_annot, out_prefix, n_samples=None, ncol=None, magma_bin='magma', run=True, **kwargs)

Run MAGMA Step II — gene-level association analysis.

Computes gene-level p-values and z-scores from GWAS SNP-level summary statistics, taking LD structure into account using a reference genotype panel. The output {out_prefix}.genes.raw is the input to both run_magma_gsa() and run_magma_gpa().

Parameters:

• bfile (str) – PLINK bfile prefix (without extension) for the LD reference panel, e.g. "g1000_eur/g1000_eur".

• pval_file (str) – GWAS p-value file. Must contain at least SNP and P columns (tab or space delimited).

• gene_annot (str) – Path to the .genes.annot file from run_magma_annotate().

• out_prefix (str) – Prefix for output files. Creates {out_prefix}.genes.raw and {out_prefix}.genes.out.

• n_samples (int | None (default: None)) – Total GWAS sample size, used when every SNP shares the same N. Passed as N=<value> in the --pval argument. Mutually exclusive with ncol — MAGMA requires exactly one of the two.

• ncol (str | None (default: None)) – Name of a column in pval_file holding a per-SNP sample size (e.g. for a meta-analysis where N varies across SNPs). Passed as ncol=<name> in the --pval argument. A column merely being named "N" is not enough on its own — MAGMA always requires an explicit N= or ncol= modifier.

• magma_bin (str (default: 'magma')) – Path to the MAGMA binary.

• run (bool (default: True)) – If False, return the command without executing.

• **kwargs – Additional flags passed verbatim to MAGMA as --key value.

Return type:

dict[str, Any]

Returns:

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

Examples

>>> run_magma_gene_analysis(
...     bfile="g1000_eur/g1000_eur",
...     pval_file="scz_gwas.txt",
...     gene_annot="results/my_gwas.genes.annot",
...     out_prefix="results/scz",
...     n_samples=67390,
... )

See also

run_magma_annotate

Step I — SNP-to-gene annotation.

run_magma_gsa

Step III — gene-set analysis.

run_magma_gpa

Step III — gene property analysis.