The exdata/ folder of this package provides a example data set
used in examples. The data are also used to validate the TopDom
implementation toward the original TopDom scripts.
The data herein contain a tiny subset of the HiC and TopDom data used in the TopDom study (Shin et al., 2016). More precisely, it contains:
A TopDom file mESC_5w_chr19.nij.HindIII.comb.40kb.domain, which
is part of the mESC_5w_domain.zip file
(5,504 bytes; md5 ffb19996f681a4d35d5c9944f2c44343) from the
Supplementary Materials of Shin et al. (2016).
These data were downloaded from the
TopDom website (http://zhoulab.usc.edu/TopDom/ - now defunct).
A normalized HiC-count matrix file nij.chr19.gz, where the
non-compressed version is part of the mESC.norm.tar.gz file
(1,305,763,679 bytes; md5 2e79d0f57463b5b7c4bf86b187086d3c) originally
downloaded from the
UCSD Ren Lab.
It is a tab-delimited file containing a 3250-by-3250 numeric matrix
non-negative decimal values. The underlying HiC sequence data is
available from
GSE35156
on GEO and was published part of Dixon, et al. (2012).
Dixon JR, Selvaraj S, Yue F, Kim A, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012 Apr 11; 485(7398):376-80, doi: 10.1038/nature11082, PMCID: PMC3356448, PMID: 22495300.
Shin, et al., TopDom: an efficient and deterministic method for identifying topological domains in genomes, Nucleic Acids Res. 2016 Apr 20; 44(7): e70., 2016. doi: 10.1093/nar/gkv1505, PMCID: PMC4838359, PMID: 26704975.