Package index • gwastargets

Pipeline generation

Generate a complete targets pipeline and Quarto report chunks from a cohort manifest.

generate_gwas_meta_pipeline(): Generate targets pipeline code for GWAS meta-analysis
generate_report_chunks(): Generate Quarto report chunks for a GWAS meta-analysis trait

Per-cohort preparation

Clean, harmonize, and QC individual cohort summary statistics.

prep_gwas(): Prepare and QC GWAS summary statistics
clean_gwas(): Clean GWAS summary statistics with tidyGWAS
harmonize_sumstats_headers(): Harmonize GWAS summary statistics headers
snp_match_munge(): Match GWAS SNPs against a reference SNP list
build_column_map(): Build a column rename map from per-cohort manifest values

Quality control

Summarize per-cohort statistics before meta-analysis.

summarize_sumstats(): Summarize GWAS summary statistics

Meta-analysis

Fixed-effects IVW meta-analysis across cohorts.

meta_analyze_ivw(): Inverse-variance weighted GWAS meta-analysis

Downstream analysis

Loci extraction, common variant identification, and MR-MEGA MDS.

extract_loci(): Extract genome-wide significant independent loci
extract_common_variants(): Extract variants common to all GWAS studies
calculate_mr_mega_mds(): Calculate MR-MEGA MDS coordinates from allele frequency data