News for Package 'protViz'

Changes in protViz version 0.7.3 (2022-04-04)

• added functions blockRandom, assignPlatePosition, insertSamples for configuring MS instrument queues.

• replaced pubmedid urls by DOIs.

• add replication code for Figures 1-5 in doi:10.1021/jasms.0c00040.

Changes in protViz version 0.6.8 (2020-04-23)

• fix #8.

• added method for centroiding a spectrum acquired in profile mode.

• fix #11.

• new by labeling using legend with fragment ion ordered by m/z values #10.

• fix #9.

Changes in protViz version 0.5.0 (2019-11-18)

• added comet.R helper functions.

• recfactored peakplot functions.

Changes in protViz version 0.4.0 (2019-01-03)

• resolve #6.

• new S3 method for fragmentIon as.data.frame.

Changes in protViz version 0.3.0 (2017-06-22)

• refactored ?findNN and ?AA man pages.

• ssrc accepts also a vector as argument.

• as.data.frame.pepxml.

Changes in protViz version 0.2.45 (2017-11-17)

• implement Rcpp module Fasta #3.

• added the Swiss-Prot P12763 protein for testing.

• added C++ STL lower_bound method.

• added orcid in DESCRIPTION file

Changes in protViz version 0.2.37 (2017-10-11)

• initial as.data.frame function.

• added unit test for ssrc function.

• deleted superfluous sigmamix data; please use https://bioconductor.org/packages/msqc1/ described in doi:10.1002/pmic.201500502.

Changes in protViz version 0.2.31 (2017-05-26)

• fixed “register native routine issue” by using tools::package_native_routine_registration_skeleton(".") and renaming .C exports to __findNN_ and __findNN #1.

• added support for Matrixce Sciense Mascot xml export; new S3classes: mascot and mascot_query.

• cosmetics on protViz.Rnw vignette file.

• added ssrc method for “Sequence Specific Retention Calculator”.

Changes in protViz version 0.2.16 (2016-06-01)

• PTM Marker Finder:

  • added PeptideSequence and modification to csv output.

Changes in protViz version 0.2.13 (2016-04-29)

• General:

  • added NEWS.Rd, CITATION.

  • changed URL.

  • fix R CMD check issues with R version 3.3.

Changes in protViz version 0.1.97

• BUG FIXES:

  • free memory computeFragmentIons.c

• Testing:

  • added more tests for deisotoper.R and fragmentIon.R.