mecfs_bio.constants.polyfun_constants

Column names used by PolyFun-provided dataframes.

The baseline-LF annotation members, LD-score members, derived annotation matrix, and precomputed prior all key variants by CHR, BP, SNP, A1, A2. A1 and A2 are REF-oriented: A1 is the hg19 reference allele (the gwaslab non-effect allele) and A2 is the alternate allele (the gwaslab effect allele).

Attributes:

• POLYFUN_A1_COL –
• POLYFUN_A2_COL –
• POLYFUN_BP_COL –
• POLYFUN_CHR_COL –
• POLYFUN_SNP_COL –
• POLYFUN_TO_GWASLAB_KEY_RENAME (dict[str, str]) –

POLYFUN_A1_COL module-attribute

POLYFUN_A1_COL = 'A1'

POLYFUN_A2_COL module-attribute

POLYFUN_A2_COL = 'A2'

POLYFUN_BP_COL module-attribute

POLYFUN_BP_COL = 'BP'

POLYFUN_CHR_COL module-attribute

POLYFUN_CHR_COL = 'CHR'

POLYFUN_SNP_COL module-attribute

POLYFUN_SNP_COL = 'SNP'

POLYFUN_TO_GWASLAB_KEY_RENAME module-attribute

POLYFUN_TO_GWASLAB_KEY_RENAME: dict[str, str] = {
    POLYFUN_CHR_COL: GWASLAB_CHROM_COL,
    POLYFUN_BP_COL: GWASLAB_POS_COL,
    POLYFUN_A1_COL: GWASLAB_NON_EFFECT_ALLELE_COL,
    POLYFUN_A2_COL: GWASLAB_EFFECT_ALLELE_COL,
}