analyzeLCMS {IPPD} | R Documentation

## 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: 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

[Package IPPD version 1.28.0 Index]