Calculate the precision, recall, and f-scores of the overlaps between two lists of GRanges objects indicating enhancer-gene relations

This function has the same functionality as the function "intersect_enhancer_gene_relations". The only difference is that this function aims to compare two lists of GRanges objects.

intersect_enhancer_gene_relations_in_batch(
  link.pairs,
  ep.ll,
  only.overlap = FALSE,
  max.score = "precision"
)

Arguments

link.pairs

The first list of GRanges objects saving enhancer-gene relations.

ep.ll

The second list of GRanges objects saving enhancer-gene relations.

only.overlap

Only consider the GRanges objects of which genes were overlapped against databases, TRUE by default.

max.score

Which score will be used to select the best query-hit pairs of GRanges objects, "precision" by default.

Value

Returns a data.frame to indicate the query-hit pairs as well as precision, recall, and f-score. The data.frame contains the following columns:

• EP: The ID of overlapped enhancer-gene pairs in databases.

• precision: The precision of the overlaps between enhancer-gene relations between enhancer regulons (eRegulons) and that in databases.

• recall: The recall of the overlaps between enhancer-gene relations between eRegulons and that in databases.

• fscore: The f-score of the overlaps between enhancer-gene relations between eRegulons and that in databases.

References

Li, Y., Ma, A., Wang, Y., Wang, C., Chen, S., Fu, H., Liu, B. and Ma, Q., 2022. Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. bioRxiv, pp.2022-12.

Gao, T., & Qian, J. (2020). EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. Nucleic acids research, 48(D1), D58-D64.

Gao, T., Zheng, Z., Pan, Y., Zhu, C., Wei, F., Yuan, J., ... & Qian, J. (2022). scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. Nucleic acids research, 50(D1), D371-D379.