cellink.resources.liftover_gwas_summary_stats

cellink.resources.liftover_gwas_summary_stats(df, source_build, target_build, chrom_col='chromosome', pos_col='base_pair_location', drop_failed=True)

Translate SNP positions in a GWAS summary-statistics DataFrame between genome builds.

Parameters:

• df (pd.DataFrame) – GWAS summary statistics DataFrame containing at least chrom_col and pos_col.

• source_build (str) – Genome build of the input positions. Accepts ‘GRCh38’/’hg38’ or ‘GRCh37’/’hg19’.

• target_build (str) – Genome build to translate positions to.

• chrom_col (str, default='chromosome') – Name of the chromosome column.

• pos_col (str, default='base_pair_location') – Name of the position column.

• drop_failed (bool, default=True) – If True, rows whose positions could not be lifted over are dropped. If False, failed positions are set to pd.NA.

Return type:

DataFrame

Returns:

pd.DataFrame Copy of df with pos_col replaced by translated positions.

Raises:

ImportError – If the liftover package is not installed.