队列表型关联与精细定位查询：参数与补充说明

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

查询日本生物样本库中的变异表型关联

dnakit.databases.bio_bank_japan_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
rsid	string	None	dbSNP rsID, e.g. 'rs7903146'. Auto-resolved to GRCh37 coordinates via Ensembl. Provide this OR 'variant'.
variant	string	None	Variant in chr:pos:ref:alt or chr-pos-ref-alt format, in GRCh37, e.g. '10:114758349:C:T'. Provide this OR 'rsid'. A bare rsID is also accepted here.
limit	integer	None	Maximum number of phenotype associations to return (sorted by ascending p-value).
max_pval	number | null	None	Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).
verbose	bool	True	运行提示开关。

查询 FinnGen 变异精细定位结果

dnakit.databases.finn_gen_get_variant_finemapping(*, variant, verbose=True)

参数	类型	必填 / 默认值	说明与约束
variant	string	必填	Genomic variant in chr:pos:ref:alt format (GRCh38). Examples: '19:44908684:T:C' (APOE rs429358), '10:112998590:C:T' (TCF7L2 rs7903146). Also accepts chr-pos-ref-alt format.
verbose	bool	True	运行提示开关。

查询基因稀有变异负荷与表型的关联

dnakit.databases.genebass_gene_burden_phewas(*, gene, burden_set=None, limit=None, max_pval=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
gene	string	必填	Ensembl gene ID (e.g. 'ENSG00000148737') or gene symbol (e.g. 'TCF7L2'). Symbols are auto-resolved via Ensembl.
burden_set	string	None	Variant category aggregated in the burden test. One of: 'pLoF' (default), 'missense|LC', 'synonymous'. Aliases accepted: lof/plof -> pLoF, missense -> missense|LC.
limit	integer	None	Maximum number of phenotype associations to return (sorted by ascending burden p-value).
max_pval	number | null	None	Optional: only return associations with burden p-value <= this threshold (e.g. 2.5e-6 for exome-wide significance).
verbose	bool	True	运行提示开关。

查询台湾精准医疗队列的变异表型关联

dnakit.databases.tpmi_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
rsid	string	None	dbSNP rsID, e.g. 'rs7903146'. Auto-resolved to GRCh38 coordinates via Ensembl. Provide this OR 'variant'.
variant	string	None	Variant in chr:pos:ref:alt or chr-pos-ref-alt format, in GRCh38, e.g. '10:112998590:C:T'. Provide this OR 'rsid'. A bare rsID is also accepted here.
limit	integer	None	Maximum number of phenotype associations to return (sorted by ascending p-value).
max_pval	number | null	None	Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).
verbose	bool	True	运行提示开关。

查询 UKB-TOPMed 的变异表型关联

dnakit.databases.ukbtopmed_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
rsid	string	None	dbSNP rsID, e.g. 'rs7903146'. Auto-resolved to GRCh38 coordinates via Ensembl. Provide this OR 'variant'.
variant	string	None	Variant in chr:pos:ref:alt or chr-pos-ref-alt format, in GRCh38, e.g. '10:112998590:C:T'. Provide this OR 'rsid'. A bare rsID is also accepted here.
limit	integer	None	Maximum number of phenotype associations to return (sorted by ascending p-value).
max_pval	number | null	None	Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).
verbose	bool	True	运行提示开关。