Calculate the p-values of overlaps between two lists of GRanges objects

Source: R/run_stream.R

This function has the same functionality as the function "intersect_peaks". The only difference is that this function compares two lists of GRanges objects and returns a data.frame composed of the IDs in each GRanges object as well as the p-values.

intersect_peaks_in_batch(x.ll, y.ll, n.times = 100)

Arguments

x.ll

The first list of GRanges objects.

y.ll

The first list of GRanges objects.

n.times

The number of times of permutation, 1000 by default.

Value

Returns a data.frame composed of the IDs of significantly overlapped GRanges objects and p-values.

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.

Gel, B., Díez-Villanueva, A., Serra, E., Buschbeck, M., Peinado, M. A., & Malinverni, R. (2016). regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics, 32(2), 289-291.