analyzeLCMS: Functionality for LC-MS data
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:
- 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
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
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