mzmatch.ipeak.convert.ConvertToText: mzmatch.ipeak.convert.ConvertToText

In mzmatch.R: mzmatch and PeakML integration for XCMS.

Description

Converts the contents of a PeakML file to a tab-separated text file.

Usage

mzmatch.ipeak.convert.ConvertToText(JHeapSize=1425, i, o, databases, annotations, h, v)

Arguments

JHeapSize	Amount of RAM memory in megabytes, which should be reserved by the Java virtual machine. The default value is 1425 megabytes.
i	The input file in the PeakML file format. When this option is not set, the input is read from the standard input.
o	The output file in text format. When this option is not set, the ouput is written to the standard out. Be sure to unset the verbose option when setting up a pipeline reading and writing from the standard in- and outputs.
databases	Optional list of database-files in the moleculedb format. These databases are used to translate the id's in the annotation 'identifications' to full molecule names.
annotations	Optional list of annotations to be exported.
h	When this is set, the help is shown.
v	When this is set, the progress is shown on the standard output.

Details

Converts the contents of a PeakML file to a tab-separated text file. In order to make the file useable in a spreadsheet environment, only the top-level data for each measurement is given in the file. This application has been extended with support for outputting annotations.

Value

This function returns no value.

Author(s)

RA Scheltema ([e-mail])

References

0. PeakML/mzMatch - a file format, Java library, R library and tool-chain for mass spectrometry data analysis. In preparation.

See Also

PeakML.xcms.read

mzmatch.R documentation built on May 31, 2017, 4:31 a.m.