S4 generic functions for Bioconductor proteomics infrastructure

S4 generic functions needed by Bioconductor proteomics
        packages.

S4 implementation of vector-like and list-like objects

The S4Vectors package defines the Vector and List virtual classes
	and a set of generic functions that extend the semantic of ordinary
	vectors and lists in R. Package developers can easily implement
	vector-like or list-like objects as concrete subclasses of Vector or
	List. In addition, a few low-level concrete subclasses of general
	interest (e.g. DataFrame, Rle, and Hits) are implemented in the
	S4Vectors package itself (many more are implemented in the IRanges
	package and in other Bioconductor infrastructure packages).

R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.23.3)

IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle

S4-utils.R show-utils.R utils.R normarg-utils.R LLint-class.R
isSorted.R subsetting-utils.R vector-utils.R integer-utils.R
character-utils.R eval-utils.R map_ranges_to_runs.R
DataTable-class.R Annotated-class.R Vector-class.R
Vector-comparison.R Vector-setops.R Vector-merge.R Hits-class.R
Hits-comparison.R Hits-setops.R Rle-class.R Rle-utils.R
List-class.R List-comparison.R List-utils.R SimpleList-class.R
HitsList-class.R DataFrame-class.R Pairs-class.R
expand-methods.R FilterRules-class.R aggregate-methods.R
shiftApply-methods.R split-methods.R zzz.R

parser for netCDF, mzXML, mzData and mzML and mzIdentML files
(mass spectrometry data)

Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

Steffen Neumann <sneumann@ipb-halle.de>,
Laurent Gatto <lg390@cam.ac.uk>,
Qiang Kou <qkou@umail.iu.edu>

mzR provides a unified API to the common file formats and
        parsers available for mass spectrometry data. It comes with a
        wrapper for the ISB random access parser for mass spectrometry
        mzXML, mzData and mzML files. The package contains the
        original code written by the ISB, and a subset of the
        proteowizard library for mzML and mzIdentML. The netCDF
        reading code has previously been used in XCMS.