Sumstats
The main GWASLab object for loading, QC, harmonization, filtering, plotting, and downstream analysis of GWAS summary statistics.
import gwaslab as gl
mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
mysumstats.basic_check()
mysumstats.harmonize(ref_seq="ref.fa")
mysumstats.plot_mqq()
API sections
| Section | Description |
|---|---|
| Core | Construction, pipelines (basic_check, harmonize), harmonization helpers, I/O |
| Fix | Standardization and QC (fix_id, fix_chr, check_sanity, …) |
| Filter | Subsetting variants (filter_value, filter_region, exclude_hla, …) |
| Plot | Visualization methods (plot_mqq, plot_region, …) |
| Downstream | Lead/novel extraction, LDSC, clumping, finemapping, PRS |
For tutorials see Sumstats Object, QC and Filtering, and Visualization.