sweepline {IPPD} | R Documentation

## Sweep line scheme to process LC-MS data

### Description

The function implements a version of the sweep line scheme suggested in Schulz-Trieglaff et al. (2008) to aggregate the results of multiple scans of an LC-MS dataset.

### Usage

    sweepline(peaklists, rt, tol = 100, gap = 2, minboxlength = 5)

### Arguments

`peaklists` | A `list` of matrices as in the slot `peaklistprocessed` of an object of class `peaklist`. It is assumed that the entries of `peaklists` correspond to the sequence retention times when ordered in ascending order.
`rt` | A `numeric` vector of retention times.
`tol` | A `m/z` tolerance (in parts per million, ppm) below which signals of different scans (retention times) are considered for merging.
`gap` | Retention time intervals are formed by merging signals of adjacent (with respect to retention time) scans. An intervals is closed (i.e. no further signals are added) once no additional signal has been added for more than `gap` consecutive scans.
`minboxlength` | Minimum number of adjacent signals found such that the corresponding retention time interval is kept in the output.

### Value

A `matrix` having the following columns. Each row corresponds to a retention time interval of consecutive signals.

`loc`

  `m/z`-position corresponding to the interval.

`charge`

  charge of the signals found.

`quant`

  Cumulative intensities of the signals found.

`rt_begin`,`rt_begin`

  Boundaries of the retention time interval.

`npeaks`

  Total number of scans containing signals assigned to the interval.

`gapcount`

  Total number of scans corresponding to the retention time interval not containing a signal.

### 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

### See Also

analyzeLCMS

[Package IPPD version 1.28.0 Index]