***********************************
CHANGES IN VERSION 1.3.3

NEW FEATURES

   o Add PCA function on Hi-C interaction map as in Lieberman-Aiden et al. 2009

BUG FIXES

   o HTCexp. Error in constructor when the interaction map has a dim = 1

   o mapC. Bug fixed in the visualization of two interaction maps of different sizes. The scale was updated, and the annotation tracks is always drawn from the larger map.


***********************************
CHANGES IN VERSION 1.3.2

NEW FEATURES

   o New visualization for HTClist objects

   o New methods for HTClist objects

   o New HTClist class to manage list of HTCexp object (basically Hi-C data)


SIGNIFICANT USER-VISIBLE CHANGES

   o Update of all man pages

   o Update of the Nora_5C data. E14 and MEF are now HTClist objects

   o Update of the importC/exportC function. The standard format is now matrix-based. This seems to be the most commonly used format.

   o Update of all mapC methods. The view parameter is removed. The HTCexp object are now displayed in the triangle view, whereas the HTClist are displayed in the heatmap view


***********************************
CHANGES IN VERSION 1.3.1

NEW FEATURES

   o MAJOR RELEASE : replace all GenomeIntervals objects by GRanges ones in order to improve the compatibility with other HT BioC packages

SIGNIFICANT USER-VISIBLE CHANGES
 
   o The ExtractRegion method has a new MARGIN parameter. The idea is the same than for any apply function. If MARGIN is equal to 1 (resp. 2, resp. c(1,2)), the region is extracted from the 'x' (resp. 'y', resp. both) intervals 
   
   o Plot function. When two HTCexp objects are plot together, only the intersection of the 'x' and 'y' intervals are used.

   o The 'range' method now returns a GRanges object

   o Changes in the data windowing for the extreme bins

   o mapC requires a HTCexp object only. Objects from the matrix class are no longer allowed

DEPRECATED AND DEFUNCT

   o seq_name is now deprecated

   o export and normPerZscore are now defunct 

BUG FIXES

   o exportC. Bug fixed in bin coordinates

   o CQC. Bug fixed with NA values

   o mapC. Bug fixed in the visualization of annotation features. Select the annotation in the same chromosome space before plotting.

   o mapC. Bug fixed in the visualization of count values for interchromosomal data 

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CHANGES IN VERSION 1.1.3

NEW FEATURES

   o Adding CITATION file

DEPRECATED AND DEFUNCT

   o Update of getExpectedCount function to use the lowess() function (stats). The 'C' call in stats is now deprecated


***********************************
CHANGES IN VERSION 1.1.2

NEW FEATURES

   o New package vignette

   o Add new normalization method - normPerTrans

   o Add importC and exportC function, to load and import csv file


SIGNIFICANT USER-VISIBLE CHANGES

   o The CQC function now returns a matrix

   o Simplify getExpectedCounts help page

   o Update of import.my5C function. Simplify the import for matrix data


DEPRECATED AND DEFUNCT

   o The export method is now replace by exportC. The standard csv format is now exported.

   o The normPerZscore method is depracted. See normPerExpected instead

   o Remove Bau et al. 5C dataset


BUG FIXES

  o isBinned. Fix bug for interchromosomal interactions

  o extracRegion. Add a chromosome parameter, and changes for interchromosomal data

  o binningC. Changes for interchromosomal maps

  o Sort xgi and ygi objects when the HTCexp constructor is called

  o Force the xgi and ygi objects to have some ids

  
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CHANGES IN VERSION 1.1.1

NEW FEATURES

   o Include the Nora et al (Nature 2012) 5C dataset (GSE35721).Two mouse samples are included in the package ; male undifferentiated ES cells (E14, GSM873935) and male embryonic fibroblasts (MEF, GSM873924). Only the cis interaction maps chrX vs chX are provided.