Skip to content

mecfs_bio.constants.fast_ct_ldsc_constants

Column and file names for the fast all-pairs CT-LDSC outputs.

The pairs table is read by GeneticCorrelationClustermapTask (p1, p2, rg, p) and by LAVA's sample-overlap reader (p1, p2, gcov_int, h2_int); the heritability table is read by the same LAVA reader (p, Intercept). Those names are therefore fixed by the readers.

Attributes:

FAST_CT_LDSC_ALIGNED_FILENAME module-attribute 

FAST_CT_LDSC_ALIGNED_FILENAME = 'aligned.parquet'

FAST_CT_LDSC_ALLELE_MISMATCH_FRACTION_COL module-attribute 

FAST_CT_LDSC_ALLELE_MISMATCH_FRACTION_COL = (
    "allele_mismatch_fraction"
)

FAST_CT_LDSC_COVERAGE_COL module-attribute 

FAST_CT_LDSC_COVERAGE_COL = 'coverage'

FAST_CT_LDSC_DIAGNOSTICS_FILENAME module-attribute 

FAST_CT_LDSC_DIAGNOSTICS_FILENAME = 'diagnostics.json'

FAST_CT_LDSC_GCOV_COL module-attribute 

FAST_CT_LDSC_GCOV_COL = 'gcov'

FAST_CT_LDSC_GCOV_INT_COL module-attribute 

FAST_CT_LDSC_GCOV_INT_COL = 'gcov_int'

FAST_CT_LDSC_GCOV_INT_SE_COL module-attribute 

FAST_CT_LDSC_GCOV_INT_SE_COL = 'gcov_int_se'

FAST_CT_LDSC_GCOV_SE_COL module-attribute 

FAST_CT_LDSC_GCOV_SE_COL = 'gcov_se'

FAST_CT_LDSC_H2_INT_COL module-attribute 

FAST_CT_LDSC_H2_INT_COL = 'h2_int'

FAST_CT_LDSC_H2_LIAB_COL module-attribute 

FAST_CT_LDSC_H2_LIAB_COL = 'h2_liab'

FAST_CT_LDSC_H2_LIAB_SE_COL module-attribute 

FAST_CT_LDSC_H2_LIAB_SE_COL = 'h2_liab_se'

FAST_CT_LDSC_H2_OBS_COL module-attribute 

FAST_CT_LDSC_H2_OBS_COL = 'h2_obs'

FAST_CT_LDSC_H2_OBS_P1_COL module-attribute 

FAST_CT_LDSC_H2_OBS_P1_COL = 'h2_obs_p1'

FAST_CT_LDSC_H2_OBS_P2_COL module-attribute 

FAST_CT_LDSC_H2_OBS_P2_COL = 'h2_obs_p2'

FAST_CT_LDSC_H2_OBS_SE_COL module-attribute 

FAST_CT_LDSC_H2_OBS_SE_COL = 'h2_obs_se'

FAST_CT_LDSC_INTERCEPT_COL module-attribute 

FAST_CT_LDSC_INTERCEPT_COL = 'Intercept'

FAST_CT_LDSC_INTERCEPT_SE_COL module-attribute 

FAST_CT_LDSC_INTERCEPT_SE_COL = 'Intercept_se'

FAST_CT_LDSC_LAMBDA_GC_COL module-attribute 

FAST_CT_LDSC_LAMBDA_GC_COL = 'lambda_gc'

FAST_CT_LDSC_MEAN_CHI2_COL module-attribute 

FAST_CT_LDSC_MEAN_CHI2_COL = 'mean_chi2'

FAST_CT_LDSC_N_BAR_COL module-attribute 

FAST_CT_LDSC_N_BAR_COL = 'n_bar'

FAST_CT_LDSC_N_COL module-attribute 

FAST_CT_LDSC_N_COL = 'n'

FAST_CT_LDSC_N_SNPS_COL module-attribute 

FAST_CT_LDSC_N_SNPS_COL = 'n_snps'

FAST_CT_LDSC_P1_COL module-attribute 

FAST_CT_LDSC_P1_COL = 'p1'

FAST_CT_LDSC_P2_COL module-attribute 

FAST_CT_LDSC_P2_COL = 'p2'

FAST_CT_LDSC_POSITION_CONCORDANCE_COL module-attribute 

FAST_CT_LDSC_POSITION_CONCORDANCE_COL = (
    "position_concordance"
)

FAST_CT_LDSC_RG_COL module-attribute 

FAST_CT_LDSC_RG_COL = 'rg'

FAST_CT_LDSC_RG_P_COL module-attribute 

FAST_CT_LDSC_RG_P_COL = 'p'

FAST_CT_LDSC_RG_SE_COL module-attribute 

FAST_CT_LDSC_RG_SE_COL = 'se'

FAST_CT_LDSC_RG_Z_COL module-attribute 

FAST_CT_LDSC_RG_Z_COL = 'z'

FAST_CT_LDSC_TRAIT_COL module-attribute 

FAST_CT_LDSC_TRAIT_COL = 'p'

FAST_CT_LDSC_Z_COL module-attribute 

FAST_CT_LDSC_Z_COL = 'z'

HAPMAP3_SNPLIST_A1_COL module-attribute 

HAPMAP3_SNPLIST_A1_COL = 'A1'

HAPMAP3_SNPLIST_A2_COL module-attribute 

HAPMAP3_SNPLIST_A2_COL = 'A2'

HAPMAP3_SNPLIST_RSID_COL module-attribute 

HAPMAP3_SNPLIST_RSID_COL = 'SNP'