analyzeLCMS: Functionality for LC-MS data

In IPPD: Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching

Description

The function analyzeLCMS applies the function getPeaklist to all scans of the dataset. The sweep line scheme of Schulz-Trieglaff et al. (2008) is then used to find retention time intervals of consecutive signals.

Usage

analyzeLCMS(data, arglist.fitModelParameters = list(),
                         arglist.getPeaklist = list(),
                         arglist.threshold = list(),
                         arglist.sweepline = list(),
                         trace = TRUE)

Arguments

data	data can be one of the following: A character for the path to the file that is to be processed. The file has to be either an mzXML file or a three-column matrix whose columns contains retention times, m/z positions and intensities (exactly in that order). An object of class mzXML. A matrix or data.frame containing three columns containing retention times, m/z positions and intensities (exactly in that order).
arglist.fitModelParameters	Optional arguments to be passed to fitModelParameters.
arglist.getPeaklist	Optional arguments to be passed to getPeaklist.
arglist.threshold	Optional arguments to be passed to the method threshold, see peaklist for details.
arglist.sweepline	Optional arguments to be passed to the function sweepline.
trace	A logical controlling whether status information is displayed.

Value

A list composed of

peaklists

A list of matrices as in the slot peaklistprocessed of an object of class peaklist. These matrices are obtained from running getPeaklist for all scans contained in data and applying hard thresholding as implemented in the method threshold.

boxes

A matrix of retention time intervals as returned as output by a call to the function sweepline.

References

0. Schulz-Trieglaff and R. Hussong and C. Groepl and A. Leinenbach and A. Hildebrandt and C. Huber and K. Reinert. (2008) Journal of Computational Biology, 15, 685-704

IPPD documentation built on April 28, 2020, 6:58 p.m.