mecfs_bio.constants.gwaslab_constants

Constants for interacting with gwaslab (https://github.com/Cloufield/gwaslab/tree/main/src/gwaslab).

Attributes:

• GWASLAB_BETA_COL –
• GWASLAB_CHISQ_COL –
• GWASLAB_CHROM_COL –
• GWASLAB_EFFECTIVE_SAMPLE_SIZE –
• GWASLAB_EFFECT_ALLELE_COL –
• GWASLAB_EFFECT_ALLELE_FREQ_COL –
• GWASLAB_EUR_1K_GENOMES_NAME_19 –
• GWASLAB_EUR_1K_GENOMES_NAME_38 (GWASLabVCFRefFile) –
• GWASLAB_HUMAN_GENOME_NAME_19 –
• GWASLAB_HUMAN_GENOME_NAME_38 –
• GWASLAB_INFO_SCORE_COL –
• GWASLAB_MLOG10P_COL –
• GWASLAB_NON_EFFECT_ALLELE_COL –
• GWASLAB_N_CASE_COL –
• GWASLAB_N_CONTROL_COL –
• GWASLAB_ODDS_RATIO_COL –
• GWASLAB_POS_COL –
• GWASLAB_P_COL –
• GWASLAB_RSID_COL –
• GWASLAB_SAMPLE_SIZE_COLUMN –
• GWASLAB_SE_COL –
• GWASLAB_SNPID_COL –
• GWASLAB_STATUS_COL –
• GWASLabVCFRefFile –
• GwaslabKnownFormat –

GWASLAB_BETA_COL module-attribute

GWASLAB_BETA_COL = 'BETA'

GWASLAB_CHISQ_COL module-attribute

GWASLAB_CHISQ_COL = 'CHISQ'

GWASLAB_CHROM_COL module-attribute

GWASLAB_CHROM_COL = 'CHR'

GWASLAB_EFFECTIVE_SAMPLE_SIZE module-attribute

GWASLAB_EFFECTIVE_SAMPLE_SIZE = 'N_EFF'

GWASLAB_EFFECT_ALLELE_COL module-attribute

GWASLAB_EFFECT_ALLELE_COL = 'EA'

GWASLAB_EFFECT_ALLELE_FREQ_COL module-attribute

GWASLAB_EFFECT_ALLELE_FREQ_COL = 'EAF'

GWASLAB_EUR_1K_GENOMES_NAME_19 module-attribute

GWASLAB_EUR_1K_GENOMES_NAME_19 = '1kg_eur_hg19'

GWASLAB_EUR_1K_GENOMES_NAME_38 module-attribute

GWASLAB_EUR_1K_GENOMES_NAME_38: GWASLabVCFRefFile = (
    "1kg_eur_hg38"
)

GWASLAB_HUMAN_GENOME_NAME_19 module-attribute

GWASLAB_HUMAN_GENOME_NAME_19 = 'ucsc_genome_hg19'

GWASLAB_HUMAN_GENOME_NAME_38 module-attribute

GWASLAB_HUMAN_GENOME_NAME_38 = 'ucsc_genome_hg38'

GWASLAB_INFO_SCORE_COL module-attribute

GWASLAB_INFO_SCORE_COL = 'INFO'

GWASLAB_MLOG10P_COL module-attribute

GWASLAB_MLOG10P_COL = 'MLOG10P'

GWASLAB_NON_EFFECT_ALLELE_COL module-attribute

GWASLAB_NON_EFFECT_ALLELE_COL = 'NEA'

GWASLAB_N_CASE_COL module-attribute

GWASLAB_N_CASE_COL = 'N_CASE'

GWASLAB_N_CONTROL_COL module-attribute

GWASLAB_N_CONTROL_COL = 'N_CONTROL'

GWASLAB_ODDS_RATIO_COL module-attribute

GWASLAB_ODDS_RATIO_COL = 'OR'

GWASLAB_POS_COL module-attribute

GWASLAB_POS_COL = 'POS'

GWASLAB_P_COL module-attribute

GWASLAB_P_COL = 'P'

GWASLAB_RSID_COL module-attribute

GWASLAB_RSID_COL = 'rsID'

GWASLAB_SAMPLE_SIZE_COLUMN module-attribute

GWASLAB_SAMPLE_SIZE_COLUMN = 'N'

GWASLAB_SE_COL module-attribute

GWASLAB_SE_COL = 'SE'

GWASLAB_SNPID_COL module-attribute

GWASLAB_SNPID_COL = 'SNPID'

GWASLAB_STATUS_COL module-attribute

GWASLAB_STATUS_COL = 'STATUS'

GWASLabVCFRefFile module-attribute

GWASLabVCFRefFile = Literal['1kg_eur_hg38', '1kg_eur_hg19']

GwaslabKnownFormat module-attribute

GwaslabKnownFormat = Literal[
    "gwaslab", "regenie", "gwascatalog"
]