read_mzIDs: Populates MS/MS results table from mzIdentML files
In MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description Usage Arguments Details Value Author(s) See Also Examples

Reads mzIdentML files into psms data.table slot of object MSnID instance. The functionality leverage mzID package facility. Note, the calls are memoised using R.cache facility. So if the call with the same list of files issues again, the results will be read from cache instead of re-parsing the mzIdentML files.

1	read_mzIDs(object, mzids, backend)

`object`	An instance of class "MSnID"
`mzids`	paths to mzIdentML (mzid) files
`backend`	Package that is leveraged for parsing. Either 'mzID' or 'mzR' corresponding to `mzID-package` and `mzR-class` respectively. The 'mzR' parser is much faster, since it is based on C++ code. 'mzID' will be kept in the package for leagacy reasons. Note, the default is 'mzID'.

mzIdentML files can be either as is or in gzip compressed form (*.mzid.gz).

Returns an instance of "MSnID" class with @psms data.table slot populated with MS/MS identifications.

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

flatten mzID

## Not run: 
msnidObj <- MSnID(".")
mzids <- system.file("extdata","c_elegans.mzid.gz",package="MSnID")
msnidObj <- read_mzIDs(msnidObj, mzids)
# clean up the cache directory
unlink(".Rcache", recursive=TRUE)

## End(Not run)