This dataExample object comprises four objects: GenomicFeatureList.GR, AnnotNames, SeqInfoChr and HTCL. All data are from Drosophila melanogaster Kc167 cells. Only data for chromosome 2L are provided.
GenomicFeatureList.GR is a list of GRanges objects, one for each genomic feature to analyze. ChIP-seq data (object GenomicFeatureList.GR) were downloaded from Gene Expression Omnibus (GEO) accessions GSE30740, GSE42085 and GSE54529. AnnotNames is a vector of the genomic feature names. SeqInfoChr is a Seqinfo object that contains chromosome 2L information.
HTCL is a HTClist object (HiTC R package) that contains a 20 kb Hi-C contact matrix Hi-C processed from Gene Expression Omnibus (GEO) accession GSE62904. This is a low resolution contact matrix just provided as an example.
data(dataExample)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.