Package: TopDom
===============

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.
 
NOTE:

 * 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/.