CHANGES IN VERSION 1.13.9

VISIBLE CHANGES in 1.13.9

  * findNeutralLossSpecs and findNeutral now accepts multiple masses and use correctly the ppm error

BUG FIXES in 1.13.9

  * Memory fix in groupCorr if all peaks are contained in one group.

CHANGES IN VERSION 1.13.8

Visible Changes in 1.13.8
  
  * Add igraph package to the dependencies

BUG FIXES in 1.13.8

  * Fix for groupCorr with graphMethod="lpc", with a igraph library > 0.6

CHANGES IN VERSION 1.13.7

BUG FIXES in 1.13.7

  * Fixed problem in findIsotopes with a previous grouped single sample xcmsSet

CHANGES IN VERSION 1.13.6

BUG FIXES in 1.13.6

  * Fixed problem in findAdducts where higher nM+x annotations were erroneous deleted
  * Fixed problem in combinexsAnnos, which produces a "subscript out of bounds " error

CHANGES IN VERSION 1.13.5

BUG FIXES in 1.13.5

  * Fixed problem "Error in data.frame(...)" in findAdducts when using polarity = negative


2012-06-12 <ckuhl@ipb-halle.de>
 * Bugfix in findIsotopes, clears 'vec' must be sorted non-decreasingly error
2012-06-11 <ckuhl@ipb-halle.de>
 * Version 1.13.4
 * Add ByteCompile: TRUE
 * Bugfix for findIsotopes, clears subscript out of bound error
2012-05-25 <ckuhl@ipb-halle.de>
 * Version 1.13.2
 * First changes for improved isotope detection
2012-04-12 <ckuhl@ipb-halle.de>
 * Version 1.13.1
 * Bugfix for findIsotopes to fix not consecutive isotope label like [M]+,[M+2]+ without [M+1]+
2012-03-19 <ckuhl@ipb-halle.de>
 * Version 1.11.10
 * Bugfix in groupCorr, where the function throws an error if argument xraw is not null
2012-03-19 <ckuhl@ipb-halle.de>
 * Version 1.11.9
 * Bugfix in findAdducts, where adduct annotation filtering was to stringent, if ips score is higher 1.5
2012-02-29 <ckuhl@ipb-halle.de>
 * Version 1.11.8
 * Bugfix in findAdducts parallel mode, where wrong psgrp indices were stored in annoGrp
2012-02-17 <ckuhl@ipb-halle.de>
 * Version 1.11.7
 * Bugfix in findAdducts, where the ruleset is not saved within a xsAnnotate object with user defined rules
 * Changed a general groupCorr behaviour. If no edge is above correlation threshold, all peaks are seperated in pspecs of size 1
2012-02-15 <ckuhl@ipb-halle.de>
 * Version 1.11.6
 * Fix error in groupCorr: If sample is set to something other than 1 or NA, it result in a crash
2012-02-10 <ckuhl@ipb-halle.de>
  * Version 1.11.5
  * Bugfix in groupCorr where parameter cor_eic_th doesn't influence correlation across samples
  * Add new parameter for groupCorr cor_exp_th
2011-12-12 <ckuhl@ipb-halle.de>
  * Version 1.11.4
  * Add missing Rd page combinexsAnnos
2011-29-11 <ckuhl@ipb-halle.de>
  * Version 1.11.3
  * Add new function combinexsAnnos. It allows checking and reannotation of sample with a coressponding sample from the opposite ion mode
2011-24-11 <ckuhl@ipb-halle.de>
  * Version 1.11.2
  * Bugfix in annotateDiffreport: Since 1.7.7 mismatch of the peaklist from CAMERA and the diffreport function results 
    in false ordered peaktable
2011-10-11 <ckuhl@ipb-halle.de>
  * Version 1.11.1
  * add the possibility to extract multiple isotope intensity from different samples
    with getIsotopeCluster
2011-20-25 <rtautenh@scripps.edu>
  * Version 1.9.9
  * added some "drop=FALSE" to fix "Error in isomatrix[, 1] : incorrect number of dimensions" error
2011-20-10 ckuhl <ckuhl@ipb-halle.de>
  * Version 1.9.8
  * Correct rule table extended_adducts_pos.csv (typo in proton mass)
2011-23-09 ckuhl <ckuhl@ipb-halle.de>
  * Version 1.9.7
  * Bugfix in calcIsotopes, causes groupCorr with calcIso to crash with (Error in rbind(resMat ...)
  * Bugfix in groupCorr with given xcmsRaw
2011-22-08 ckuhl <ckuhl@ipb-halle.de>
  * Version 1.9.6
  * Bugfix in plotEICs (Error in pks[, 1] : incorrect number of dimensions)
2011-02-08 ckuhl <ckuhl@ipb-halle.de>
  * Version 1.9.5
  * Bugfix for findIsotopes if ppm was very high it could occur that one peak is assigned as two or more isotope peaks
2011-02-08 ckuhl <ckuhl@ipb-halle.de>
  * Version 1.9.4
  * Add parameter polarity to xsAnnotate constructor
  * getPeaklist and getpspectra returns now correct annotation of negative charged ions [M]-
  * Add snow as additonal possibilty for parallel processing
  * Add function cleanParallel to clean up with spawned slave processes
2011-24-05 ckuhl <ckuhl@ipb-halle.de>
	* Fix bug in findIsotopes, which could cause a crash, if maxiso was higher than 3 
2011-12-05 ckuhl <ckuhl@ipb-halle.de>
	* plotPsSpectrum now accepts additional parameters for plot
2011-28-04 ckuhl <ckuhl@ipb-halle.de>
	* Fix bug in getpspectra, which incorrect label isotope peaks
2011-04-04 ckuhl <ckuhl@ipb-halle.de>
	* Fix bug in findAdducts, if pseudospectrum mass list has only NA values
2010-23-11 ckuhl <ckuhl@ipb-halle.de>
	* Fix bug in findAdducts. Function failed, if run in parallel mode.
2010-08-11 ckuhl <ckuhl@ipb-halle.de>
	* Add intval parameter to groupFWHM and findIsotopes
2010-08-11 ckuhl <ckuhl@ipb-halle.de>
	* Change getPeaklist to S4 Methods.
	* Add getPeaklist parameter intval, where the intensity value can be selected
2010-08-11 ckuhl <ckuhl@ipb-halle.de>
	* Additional bugfix for findIsotopes. Could occur with 1.7.1, that all isotopes will be deleted.
2010-01-11 ckuhl <ckuhl@ipb-halle.de>
	* Fix bug in findIsotopes. Occurs if the first isotope peak, could be assigned from two different monoisotopic peaks.
	* Reduce slightly the number of found isotopes
2010-11-10 ckuhl <ckuhl@ipb-halle.de>
	* Rewrite Vignette
2010-29-09 ckuhl <ckuhl@ipb-halle.de>
    	* Add function findNeutralLoss and findNeutralLossSpecs
2010-20-09 ckuhl <ckuhl@ipb-halle.de>
        * Add function getIsotopeCluster for retrival of isotope cluster
2010-11-06 ckuhl <ckuhl@ipb-halle.de>
	* Speed up in findAdducts
	* Fix unit tests
2010-05-03 ckuhl <ckuhl@ipb-halle.de>
	* Fix bug in findIsotopes, crashed with dim error
2010-04-20 ckuhl <ckuhl@ipb-halle.de>
        * Fix bug in annotate function
2010-04-19 ckuhl <ckuhl@ipb-halle.de>
	* Last changes for the next BioC release
	* Rewrite of the vignette
2010-03-17 ckuhl <ckuhl@ipb-halle.de>
	* Hugh changes in CAMERA for working with multiple sample
	* Add check constrains in groupCorr for isotopes and primary adducts
2009-11-24 ckuhl <ckuhl@ipb-halle.de>
        * Add experimental parallel mode with MPI
2009-11-20 ckuhl <ckuhl@ipb-halle.de>
        * Fix bug in setting ruletable
2009-08-26 ckuhl <ckuhl@ipb-halle.de>
        * add nSlaves as argument to findAdducts (for parallel annotation with MPI)
2009-08-24 ckuhl	<ckuhl@ipb-halle.de>
	* small bugfixes in getPeaklist
	* add neutral losses to rule set
2009-08-12 Steffen Neumann <sneumann@@ipb-halle.de>
	* Fixed plotEICs for 1 peak groups
2009-08-04 ckuhl	<ckuhl@ipb-halle.de>
	* Add ips Score to annoGrp
2009-06-03 Steffen Neumann <sneumann@@ipb-halle.de>
        * Add adduct labels to plotPeaks()
        * Add adduct labels to plotEICs()
2009-05-22 Steffen Neumann <sneumann@@ipb-halle.de>
        * Add first visualisation function plotEICs() and plotPeaks()
2009-05-06 ckuhl    <ckuhl@ipb-halle.de>
        * bump for devel 2.5
2009-03-30 ckuhl    <ckuhl@ipb-halle.de>
        * add combine_xsanno
        * small refactoring
        * changes in scoring schemata
2009-03-18 ckuhl	<ckuhl@ipb-halle.de>
	* after groupCorr every peak is now member of a group
        * bugfix: remove xM-xH clones
        * remove dependency on Hmisc
2009-03-10 ckuhl	<ckuhl@ipb-halle.de>
	* speed-up of findAdducts
2009-02-24 ckuhl        <ckuhl@ipb-halle.de>
        * refactoring findAdducts
        * add methods for pos/neg polarity comparison
2009-02-20 ckuhl        <ckuhl@ipb-halle.de>
        * replace na.omit with naOmit
2009-02-18 ckuhl	<ckuhl@ipb-halle.de>
	* add neutral losses into ruleset
	* other bugfixes
2009-01-19 ckuhl	<ckuhl@ipb-halle.de>
	* Change isotope nomination
	* add lists for fragments, ions and neutral losses
2008-10-15  ckuhl	<ckuhl@ipb-halle.de>
	* Lot of bugfixes and speed up the correlation
2008-10-13  ckuhl	<ckuhl@ipb-halle.de>
	* First build for version 0.1.1
2007-10-12  sneumann  <sneumann@ipb-halle.de>
	* Inital release & collection of stuff
