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

1
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