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)

[Package MSnID version 1.28.0 Index]