ramp: High-performance, low-level access to mzXML/mzData files

In sneumann/xcms-presvnbridge: LC/MS and GC/MS Data Analysis

Description

Functions for low-level access to data in mzXML/mzData files. They have been optimized for maximum speed and memory efficiency.

Usage

rampInit()
rampPrintFiles()
rampIsFile(filename)
rampOpen(filename)
rampClose(rampid)
rampCloseAll()
rampNumScans(rampid)
rampScanHeaders(rampid)
rampSIPeaks(rampid, seqNum, peaksCount)
rampRawData(rampid)

Arguments

filename	path to mxXML/mzData file
rampid	RAMP file ID
seqNum	integer vector with indecies of scans to read
peaksCount	integer vector with number of peaks in each scan to read

Details

The mechanisms and structure of mzXML/mzData files are not discussed here, please see the mzXML/mzData documentation for more information. These functions make use of the RAMP (Random Access Minimal Parser) code from the SASHIMI open-source project.

rampInit initializes the data structures used for holding RAMP file pointers and indices.

rampPrintFiles prints out a list of all files currently open.

rampCloseAll closes all mzXML/mzData files and frees memory associated with their indices.

Value

rampIsFile returns TRUE if the referenced file is an mzXML or mzData file and FALSE otherwise.

rampOpen returns the rampid of the opened file.

rampClose returns the closing status.

rampNumScans returns the number of scans with an msLevel of 1.

rampSIPeaks returns a named list with components scanindex, mz, and intensity.

rampScanHeaders returns a data frame with header information for each scan.

rampRawData returns a named list with components rt, tic, scanindex, mz and intensity.

rampRawDataMSn returns a named list with components of MSn data rt, acquisitionNum, precursorMZ, precursorIntensity peaksCount, msLevel, precursorCharge, scanindex, collisionEnergy, mz and intensity.

An error in any of the functions will return a (negative) integer error code.

Author(s)

Colin A. Smith, [e-mail]

References

mzXML file format: http://sashimi.sourceforge.net/software_glossolalia.html

mzData file format: http://psidev.sourceforge.net/ms/index.html

Examples

	## Not run: 
	library(msdata)
	mzdatapath <- system.file("iontrap", package = "msdata")
	mzdatafiles<-list.files(mzdatapath, pattern = "extracted.mzData", recursive = TRUE, full.names = TRUE)
	mzdatafiles
	id<-xcms:::rampOpen(mzdatafiles)
	id

	head<-xcms:::rampScanHeaders(id)
	MS1data<-xcms:::rampRawData(id)
	MS2data<-xcms:::rampRawDataMSn(id)
	xcms:::rampClose(id)
	str(MS2data)
	str(MS1data)
	str(head)
	
## End(Not run)

sneumann/xcms-presvnbridge documentation built on May 30, 2019, 6:02 a.m.