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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


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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.