cellink.tl.external.run_magma_pipeline

cellink.tl.external.run_magma_pipeline(gwas_sumstats, output_prefix='magma_results', genome_build='GRCh38', gene_id_type='ensembl', window_size=(35, 10), n_samples=None, ld_source=None, dd=None, reference_panel=None, external_ld_prefix=None, col_mapping=None, config_file='configs/magma.yaml', magma_bin='magma')

Complete MAGMA pipeline: prepare inputs, annotate SNPs, and run gene analysis.

Parameters:

• gwas_sumstats (pd.DataFrame) – GWAS summary statistics.

• output_prefix (str) – Prefix for all output files.

• genome_build (str) – ‘GRCh37’ or ‘GRCh38’.

• gene_id_type (str) – Gene ID type: ‘entrez’, ‘ensembl’, or ‘gene_name’.

• window_size (tuple of int) – Upstream/downstream window in kilobases for SNP-to-gene annotation.

• n_samples (int) – GWAS sample size.

• ld_source (str or None) – LD reference strategy — see prepare_magma_inputs for full docs. - ‘dd_genotypes’ : use genotypes from DonorData (pass dd) - ‘reference_panel’: download a 1000G panel (pass reference_panel) - ‘external’ : use existing PLINK files (pass external_ld_prefix) - None : raises an error — LD reference is required for gene analysis

• dd (DonorData, optional) – Required when ld_source=’dd_genotypes’.

• reference_panel (str, optional) – Required when ld_source=’reference_panel’. Options: ‘EUR’, ‘EAS’, ‘AFR’.

• external_ld_prefix (str or Path, optional) – Required when ld_source=’external’. Path prefix of PLINK files.

• col_mapping (dict, optional) – Column rename mapping for GWAS sumstats.

• config_file (str) – Path to YAML config.

• magma_bin (str) – Path to MAGMA binary.

Return type:

Path

Returns:

Path Path to gene-level results file (.genes.out).

Examples

>>> # Using your own cohort's genotypes
>>> results = run_magma_pipeline(
...     gwas_df, output_prefix="t2d", n_samples=100000,
...     ld_source="dd_genotypes", dd=my_donor_data,
...     magma_bin="./magma/magma",
... )

>>> # Using a downloaded 1000G panel
>>> results = run_magma_pipeline(
...     gwas_df, output_prefix="t2d", n_samples=100000,
...     ld_source="reference_panel", reference_panel="EUR",
... )

>>> # Using your own pre-built PLINK reference
>>> results = run_magma_pipeline(
...     gwas_df, output_prefix="t2d", n_samples=100000,
...     ld_source="external", external_ld_prefix="/data/my_ref_panel",
... )