NEWS

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MSnID 1.18.1

• Improved protein inference. Now it has two options - either unique peptide or with razor.

MSnID 1.17.1

• Broadened the scope of the tool to ImmunoOncology - that is finding rare events that reflected in protein sequence.

MSnID 1.15.1

• 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.

MSnID 1.11.1

• 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

MSnID 1.7.3

• 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.
• Added unit test to cover new PSM FDR calculation.

MSnID 1.7.2

• added high performance parser based on mzR::openIDFile

MSnID 1.7.1

• added infer_parsimonious_accessions method
• version leap from 1.3.1 to 1.7.1 to catch up with Bioconductor
• fixed conflict between reshape2 and data.table

MSnID 1.3.1

• S4 methods "accessions" and "proteins" outsourced to ProtGenerics

MSnID 1.1.6

• Added explicit mc.cores argument for "Grid" type of optimization
• Fix of trimming to basename on POSIX

MSnID 1.1.5

• Always trimming spectrumFile and databaseFile to basename after reading data from mzIdentML files.

MSnID 1.1.4

• Catching up with changes in mzID package version 1.5.3

MSnID 1.1.3

• Updated data, documentation and unit test to reflect the latest changes in mzID

MSnID 1.1.2

• 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.
• added Laurent Gatto as a contributor

MSnID 1.1.1

• fix mishandling PSM
• use mzR::psms generic

MSnID 1.1.0

• Bumping versions after creating 3.0 release branch.

MSnID 0.99.3

• Rcpp back into "Depends"

MSnID 0.99.2

• Updated Rcpp dependency
• Updated contact info to match the bioc-devel mailing list

MSnID 0.99.1

• Updated dependency on mzID version

MSnID 0.99.0

• Minor bug fixes
• Added unit tests for filter optimization and assessment of non-tryptic and missed cleavages
• Version bump for Bioconductor submission

MSnID 0.1.0

• First release version