Version 1.18.1 ------------- o Improved protein inference. Now it has two options - either unique peptide or with razor. Version 1.17.1 ------------- o Broadened the scope of the tool to ImmunoOncology - that is finding rare events that reflected in protein sequence. Version 1.15.1 ------------- o mzR now added scan number(s) into the table representation of mzIdentML object. As a results it caused an error in my unit test checking if the file reads properly. Fixed this check with updated hash. Version 1.11.1 ------------- o Switch from mclapply to parLapply in filter optimizaition. This fixes a bug "Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null." Also allows to run parallel on Window OS Version 1.7.3 ------------- o Logical error fix in PSM FDR calculation. Prior it ignored redundancy in peptide to protein mapping. Now protein accession are discarded and unique rows considered before compuring the FDR. o Added unit test to cover new PSM FDR calculation. Version 1.7.2 ------------- o added high performance parser based on mzR::openIDFile Version 1.7.1 ------------- o added infer_parsimonious_accessions method o version leap from 1.3.1 to 1.7.1 to catch up with Bioconductor o fixed conflict between reshape2 and data.table Version 1.3.1 ------------- o S4 methods "accessions" and "proteins" outsourced to ProtGenerics Version 1.1.6 ------------- o Added explicit mc.cores argument for "Grid" type of optimization o Fix of trimming to basename on POSIX Version 1.1.5 ------------- o Always trimming spectrumFile and databaseFile to basename after reading data from mzIdentML files. Version 1.1.4 ------------- o Catching up with changes in mzID package version 1.5.3 Version 1.1.3 ------------- o Updated data, documentation and unit test to reflect the latest changes in mzID Version 1.1.2 ------------- o id_quality and evaluate_filter may have multiple values for the level argument. By default it is all three: "PSM", "peptide" and "accession". The return value for both methods is switched to matrices. o added Laurent Gatto as a contributor Version 1.1.1 ------------- o fix mishandling PSM o use mzR::psms generic Version 1.1.0 ------------- o Bumping versions after creating 3.0 release branch. Version 0.99.3 -------------- o Rcpp back into "Depends" Version 0.99.2 -------------- o Updated Rcpp dependency o Updated contact info to match the bioc-devel mailing list Version 0.99.1 -------------- o Updated dependency on mzID version Version 0.99.0 -------------- o Minor bug fixes o Added unit tests for filter optimization and assessment of non-tryptic and missed cleavages o Version bump for Bioconductor submission Version 0.1.0 -------------- o First release version