2012-03-19 * Version 1.11.10 * Bugfix in groupCorr, where the function throws an error if argument xraw is not null 2012-03-19 * Version 1.11.9 * Bugfix in findAdducts, where adduct annotation filtering was to stringent, if ips score is higher 1.5 2012-02-29 * Version 1.11.8 * Bugfix in findAdducts parallel mode, where wrong psgrp indices were stored in annoGrp 2012-02-17 * 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 * 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 * 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 * Version 1.11.4 * Add missing Rd page combinexsAnnos 2011-29-11 * 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 * 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 * Version 1.11.1 * add the possibility to extract multiple isotope intensity from different samples with getIsotopeCluster 2011-20-25 * Version 1.9.9 * added some "drop=FALSE" to fix "Error in isomatrix[, 1] : incorrect number of dimensions" error 2011-20-10 ckuhl * Version 1.9.8 * Correct rule table extended_adducts_pos.csv (typo in proton mass) 2011-23-09 ckuhl * 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 * Version 1.9.6 * Bugfix in plotEICs (Error in pks[, 1] : incorrect number of dimensions) 2011-02-08 ckuhl * 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 * 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 * Fix bug in findIsotopes, which could cause a crash, if maxiso was higher than 3 2011-12-05 ckuhl * plotPsSpectrum now accepts additional parameters for plot 2011-28-04 ckuhl * Fix bug in getpspectra, which incorrect label isotope peaks 2011-04-04 ckuhl * Fix bug in findAdducts, if pseudospectrum mass list has only NA values 2010-23-11 ckuhl * Fix bug in findAdducts. Function failed, if run in parallel mode. 2010-08-11 ckuhl * Add intval parameter to groupFWHM and findIsotopes 2010-08-11 ckuhl * Change getPeaklist to S4 Methods. * Add getPeaklist parameter intval, where the intensity value can be selected 2010-08-11 ckuhl * Additional bugfix for findIsotopes. Could occur with 1.7.1, that all isotopes will be deleted. 2010-01-11 ckuhl * 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 * Rewrite Vignette 2010-29-09 ckuhl * Add function findNeutralLoss and findNeutralLossSpecs 2010-20-09 ckuhl * Add function getIsotopeCluster for retrival of isotope cluster 2010-11-06 ckuhl * Speed up in findAdducts * Fix unit tests 2010-05-03 ckuhl * Fix bug in findIsotopes, crashed with dim error 2010-04-20 ckuhl * Fix bug in annotate function 2010-04-19 ckuhl * Last changes for the next BioC release * Rewrite of the vignette 2010-03-17 ckuhl * Hugh changes in CAMERA for working with multiple sample * Add check constrains in groupCorr for isotopes and primary adducts 2009-11-24 ckuhl * Add experimental parallel mode with MPI 2009-11-20 ckuhl * Fix bug in setting ruletable 2009-08-26 ckuhl * add nSlaves as argument to findAdducts (for parallel annotation with MPI) 2009-08-24 ckuhl * small bugfixes in getPeaklist * add neutral losses to rule set 2009-08-12 Steffen Neumann * Fixed plotEICs for 1 peak groups 2009-08-04 ckuhl * Add ips Score to annoGrp 2009-06-03 Steffen Neumann * Add adduct labels to plotPeaks() * Add adduct labels to plotEICs() 2009-05-22 Steffen Neumann * Add first visualisation function plotEICs() and plotPeaks() 2009-05-06 ckuhl * bump for devel 2.5 2009-03-30 ckuhl * add combine_xsanno * small refactoring * changes in scoring schemata 2009-03-18 ckuhl * after groupCorr every peak is now member of a group * bugfix: remove xM-xH clones * remove dependency on Hmisc 2009-03-10 ckuhl * speed-up of findAdducts 2009-02-24 ckuhl * refactoring findAdducts * add methods for pos/neg polarity comparison 2009-02-20 ckuhl * replace na.omit with naOmit 2009-02-18 ckuhl * add neutral losses into ruleset * other bugfixes 2009-01-19 ckuhl * Change isotope nomination * add lists for fragments, ions and neutral losses 2008-10-15 ckuhl * Lot of bugfixes and speed up the correlation 2008-10-13 ckuhl * First build for version 0.1.1 2007-10-12 sneumann * Inital release & collection of stuff