NEWS.md

In TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

Version 0.10.2 [2026-08-30]

Bug Fixes

• TopDom() no longer produces a warning object 'idxs' not found when called on data where no region can be processed, e.g. when every non-gap run of bins is shorter than the minimum region size.

• TopDom() with statFilter = TRUE (default) on extremely sparse data used to fail deep inside stats::wilcox.test() with an obscure not enough (finite) 'x' observations error. It now fails early with an informative message explaining that the data is too sparse for the statistical-filtering step and suggesting remedies such as statFilter = FALSE or a larger bin size.

• TopDom() with statFilter = TRUE (default) on a very large contact matrix (more than sqrt(.Machine$integer.max), i.e. 46340, bins) used to fail with an obscure 'to' must be a finite number error from seq(), preceded by an NAs produced by integer overflow warning, because the internal n_bins * n_bins index arithmetic overflowed R's integer range. It now fails early with an informative message suggesting statFilter = FALSE or a larger bin size.

Miscellaneous

• Increased the package test coverage from 47% to 63%, adding tests for countsPerRegion(), subsetByRegion(), readHiC(), ggCountHeatmap(), ggDomain(), ggDomainLabel(), legacy(), the overlapScores() methods, several TopDom() options (statFilter, outFile, debug, file-path input), and internal utility functions.

Documentation

• Fix equation format issue and update one URL.

• Drop stale and redirecting URLs (dead lab-software and USC library pages, PubMed/PMC links) in the help pages and README, keeping DOIs for the cited publications.

Version 0.10.1 [2020-05-04]

CRAN Policies

• Update URL that otherwise redirects HTTP to HTTPS.

Version 0.10.0 [2020-05-03]

New Features

• Package now includes mouse Chr19 data from the TopDom study. They can be found in the system.file("exdata", package = "TopDom") folder.

• The orignal TopDom scripts TopDom_v0.0.1.R and TopDom_v0.0.2.R are now distributed part of the package as-is. They can be found in the system.file("original-scripts", package = "TopDom") folder.

• readHiC() gained arguments ... which is passed as-is to read.table().

Version 0.9.1 [2020-04-02]

Bug Fixes

• ggCountHeatmap() for TopDomData could produce a warning on a partial argument name.

Version 0.9.0 [2020-02-19]

Significant Changes

• The list data.frame elements returned by overlapScores() now has column chromosome as the first position. The data.frame:s are of kind tibble.

New Features

• Add as_tibble() for TopDomOverlapScores.

Documentation

• Add further documentation on the window.size parameter.

• Add reference to Hanjun Shin's PhD thesis.

Version 0.8.2 [2019-12-17]

Documentation

• Improved help on overlapScores() and TopDom().

• Provide a reference for the default value for window.size of TopDom().

Version 0.8.1 [2019-06-19]

Software Quality

• Fix two cases of partial argument name.

Version 0.8.0 [2019-04-11]

New Features

• The TopDom object returned by TopDom() now has an attribute parameters which records the value of arguments window.size and statFilter.

• Made TopDom() faster and more memory efficient by lower the number of replicated computations.

Version 0.7.1 [2019-04-09]

Robustness

• Add internal sanity checks to TopDom() asserting that the intermediate and final results are of proper length and does not contain missing values.

Bug Fixes

• Internal Convert.Bin.To.Domain.TMP() used by TopDom() could produce Error in[<-.data.frame(tmp, , "to.coord", value = c(NA, 2500, 247500 : replacement has 3 rows, data has 1, because it assumed at least one domain was identified.

Version 0.7.0 [2019-03-15]

Significant Changes

• Renamed fields returned by overlapScores() to be in singular form, e.g. best_score instead of best_scores.

New Features

• Now overlapScores() returns also the lengths of the reference domains.

Version 0.6.0 [2019-01-08]

Significant Changes

• Renamed and swapped the order of the first two arguments of overlapScores() and renamed the second argument to reference. This was done in order to make it clear which set of topological domains the overlap scores are calculated relative to.

Version 0.5.0 [2018-11-12]

Significant Changes

• Lead TopDom author Xianghong Jasmine Zhou confirms by email that the original TopDom scripts, and thereby this package, may be released under the GNU Public License (GPL).

Version 0.4.0 [2018-10-23]

New Features

• Add countsPerRegion() for calculating the total contact-frequency counts per region specified, e.g. per domain.

• Add print(), dim(), [(), and subsetByRegion() for TopDom objects where the number of rows in the dimension reflect the number of TopDom domains.

Version 0.3.0 [2018-10-08]

New Features

• The legacy TopDom() functions, available via legacy(), also accept TopDomData objects as returned by readHiC(). This is supported mostly to make it possible to efficiently compare the different implementations.

• Added [() for TopDomData objects, e.g. tdd[1:100].

• Added subsetByRegion() for TopDomData objects.

• Added ggCountHeatmap(), ggDomain(), and ggDomainLabel() for TopDomData objects.

Version 0.2.0 [2018-07-26]

Significant Changes

• See 'BUG FIXES' below.

New Features

• Add function legacy() for access to the original TopDom v0.0.1 and TopDom v0.0.2 implementations, e.g. TopDom::legacy("0.0.1")$TopDom().

Bug Fixes

• All TopDom functions except TopDom() itself were the ones from TopDom v0.0.2.

Version 0.1.2 [2018-06-28]

Significant Changes

• Released on GitHub.

Miscellaneous

• The license of the underlying TopDom R code/scripts is still unknown, i.e. to be decided by the original authors of TopDom. Any mentioning of code licenses in this package / git repository history is invalid.

New Features

• Add overlapScores().

• Add image() for TopDomData.

• List returned by TopDom() gained class TopDom.

• Added logical option TopDom.debug, which controls whether functions produce debug output or not. The default is FALSE.

Documentation

• Updated the 'Value' section of help("TopDom") with details from the TopDom Manual (an online PDF) provided by Shin et al.

Version 0.1.1 [2018-05-04]

New Features

• Add print() method for TopDomData object.

• Reference the TopDom paper (Shin et al., 2016) in the help and the README.

Version 0.1.0 [2018-04-23]

Significant Changes

• Turned the original TopDom R script into a package.

• All progress messages are outputted done to standard error.

• Add readHiC().

New Features

• TopDom() can now read, via readHiC(), a pure count matrix file without bin information. To read such files, specify what chromosome is being read (argument chr) and the bin size of the count matrix (argument binSize).

• If the matrix file is not of a known format, then TopDom() produces an informative error. Previously it gave a message on stdout and returned 0.

Code Style

• Tidied up code.

Software Quality

• Added package tests.

Version 0.0.2 [2016-07-08]

• TopDom v0.0.2 script from http://zhoulab.usc.edu/TopDom/ with the below entries from the official release note:

• Gap Identification module is changed.

• Minor bug related to Change Points identification in very small regions is fixed.

• bed format support.

Version 0.0.1 [2015-11-09]

• TopDom v0.0.1 script from http://zhoulab.usc.edu/TopDom/.

TopDom documentation built on Aug. 31, 2026, 5:06 p.m.