mzML2dataTable: Import a mzML file and format the data into a data.table

In pmbrophy/mzDataTable: Import and convert raw mass spectrometry data formats

Description

Convert mzML/mzXML data files into data.tables. This function is used by other converters in this package and provides flexible inputs - see parameters for details.

Usage

mzML2dataTable(path, scans = NULL, header = NULL)

Arguments

path	Either a system path to the .mzML file or mzR pointer object
scans	A numeric vecotr specifying which scans to return. Optional argument. If ommited, all peaks are returned. Default is 'NULL'
header	Option to provide a header data.frame/data.table if it has already been imported. Expects header spans range of 'scans'. Default is NULL.

Value

a data.table

Examples

## Not run: 
#Typical use for user - import mzML/mzXML data as data.table
dt <- mzML2dataTable(path = "mzML_path.mzML", scans = c(1:100))

#Typical use for other functions in this package
#-import mzML/mzXML data as data.table from mzR pointer
mzML <- mzR::openMSfile(filename = "mzML_path.mzML")
dt <- mzML2dataTable(path = mzML, scans = c(1:100))

#-import mzML/mzXML scan data with previously imported header
header <- mzR::header(object = mzML, scans = c(1:100))
dt <- mzML2dataTable(path = mzML,
                     scans = c(1:100),
                     header = header)

## End(Not run)

pmbrophy/mzDataTable documentation built on June 6, 2020, 7:43 a.m.