gnomad.resources.grch38.reference_data
Return a table with annotations from the latest version of the corresponding truth data. |
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Transform methylation level from the GRCh38 methylation resource to a 0-2 scale. |
- gnomad.resources.grch38.reference_data.get_truth_ht()[source]
Return a table with annotations from the latest version of the corresponding truth data.
- The following annotations are included:
hapmap
kgp_omni (1000 Genomes intersection Onni 2.5M array)
kgp_phase_1_hc (high confidence sites in 1000 genonmes)
mills (Mills & Devine indels)
- Return type:
- Returns:
A table with the latest version of popular truth data annotations
- gnomad.resources.grch38.reference_data.transform_grch38_methylation(ht=None, methylation_expr=None)[source]
Transform methylation level from the GRCh38 methylation resource to a 0-2 scale.
Note
One of ht or methylation_expr must be provided.
The GRCh38 methylation resource provides a score ranging from 0 to 15 for autosomes. The determination of this score is described in Chen et al: https://www.biorxiv.org/content/10.1101/2022.03.20.485034v2.full For chrX, methylation scores range from 0 to 12, but these scores are not directly comparable to the autosome scores (chrX and autosomes were analyzed separately and levels are relative). Cutoffs to translate these scores to the 0-2 methylation level were determined by correlating these scores with the GRCh37 liftover scores. Proposed cutoffs are: 0, 1-5, 6+ for autosomes, and 0, 1-3, 4+ for chrX.
- Parameters:
ht (
Optional[Table]) – Optional Hail Table with methylation data. Default is None.methylation_expr (
Optional[NumericExpression]) – Optional methylation level expression. Default is None.
- Return type:
Union[Table,NumericExpression]- Returns:
Transformed methylation level expression or annotated Hail Table.