dataExample: Read chromatin domain bed file

In HiCfeat: Multiple Logistic Regression for 3D Chromatin Domain Border Analysis

Description

This dataExample object comprises three objects: GenomicFeatureList.GR, AnnotNames and Domains.GR. GenomicFeatureList.GR is a list of GRanges objects, one for each genomic feature to analyze. AnnotNames is a vector of the genomic feature names. Domains.GR is a GRanges object for topologically associating domains.

Topologically associating domains (object Domains.GR) were computed from Hi-C experiments on Drosophila melanogaster Kc167 cells from Gene Expression Omnibus (GEO) accession GSE62904. ChIP-seq data (object GenomicFeatureList.GR) on Drosophila melanogaster Kc167 cells were downloaded from Gene Expression Omnibus (GEO) accessions GSE30740, GSE42085 and GSE54529. Only data for chromosome 2L are provided.

Usage

data(dataExample)

Author(s)

Raphael Mourad

References

Kevin Van Bortle, Michael H. Nichols, Li Li, Chin-Tong Ong, Naomi Takenaka, Zhaohui S. Qin, and Victor G. Corces. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biology, 15(5):R82+, June 2014.

Li Li, Xiaowen Lyu, Chunhui Hou, Naomi Takenaka, Huy Q. Nguyen, Chin-Tong Ong, Caelin Cubenas-Potts, Ming Hu, Elissa P. Lei, Giovanni Bosco, Zhaohui S. Qin and Victor G. Corces. Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing. Molecular Cell, 15:S1097-2765, March 2015.

HiCfeat documentation built on May 2, 2019, 2:11 a.m.