hic_example_data: Example HiC dataset

In ComputationalRegulatoryGenomicsICL/GenomicInteractions-new: Utilities for handling genomic interaction data

Example HiC dataset

Description

This dataset contains HiC data from Seitan et al. 2013. The data was analysed using HOMER (Heinz et al. 2010) at a resolution of 100kb to find significant interactions. This example dataset has been filtered to retain only interactions on chromosomes 14 and 15 with a FDR < 0.1. The data has also been annotated for overlaps with Refseq promoters. See the HiC analysis vignette (vignettes(GenomicInteractions)) for more information on how this dataset was created.

Usage

data(hic_example_data)

Format

A GenomicInteractions object with length 8171.

Value

GenomicInteractions object

References

Seitan, V. C. et al. Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments. Genome Res. 23, 2066-77 (2013).

Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589.

ComputationalRegulatoryGenomicsICL/GenomicInteractions-new documentation built on April 10, 2022, 5:39 p.m.