For files under Index of /pub/databases/opentargets/genetics/latest/v2g/, what does each of the field mean? For instance, what’s interval score, what’s interval score q? Are these files of the same kind or different kinds?
Also, are the PCHi-C files available?
Thanks in advance!
Can anyone please help? Thanks!
Hi @Mousheng_Xu!
I have checked with the Genetics team, and they have told me the following regarding the fpred_scores, interval_score, and interval_score_q:
The fpred scores refer to VEP annotations.
interval_score refers to “interval”-type data that links regions to genes; this can include promoter-capture Hi-C data, DHS enhancer-promoter correlation, and FANTOM5 transcribed enhancer-promoter correlations.
interval_score likely refers to a raw score for the given data type, while interval_score_q is a quantile normalised score (i.e. 0 - 1).
As an example:
alt_allele | C
chr_id | 5
d | null
distance_score | null
distance_score_q | null
feature | unspecified
fpred_labels | [upstream_gene_variant, intron_variant]
fpred_max_label | intron_variant
fpred_max_score | 0.1
fpred_scores | [0.0, 0.1]
gene_id | ENSG00000169194
interval_score | null
interval_score_q | null
position | 132656919
qtl_beta | null
qtl_pval | null
qtl_score | null
qtl_score_q | null
qtl_se | null
ref_allele | A
source_id | vep
type_id | fpred