read_mzIDs {MSnID}

R Documentation

Populates MS/MS results table from mzIdentML files

Description

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.

Usage

    read_mzIDs(object, mzids, backend)

Arguments

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'.

Details

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

Value

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

Author(s)

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

See Also

flatten mzID

Examples

## 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)

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