mzagglom: Agglomerative partitioning of raw LC-HRMS measurements

In enviPick: Peak Picking for High Resolution Mass Spectrometry Data

Description

Agglomerative partitioning of LC-HRMS measurements. Preparatory step for mzclust and mzpick. Requires an MSlist initilialized by readMSdata as input.

Usage

	mzagglom(MSlist, dmzgap = 10,  ppm = TRUE, drtgap = 500, minpeak = 4, 
	maxint=1E7, progbar=FALSE)

Arguments

MSlist	MSlist generated by readMSdata
dmzgap	m/z gap width for partitioning
ppm	dmzgap given in ppm (TRUE) or as absolute value (FALSE)?
drtgap	RT gap width for partitioning
minpeak	Minimum number of measurements in a partition
maxint	Measurements equal or above this intensity will be retained even if ranging below minpeak
progbar	For debugging, ignore

Details

Partitioning of the full set of measurements into subsets is necessary to speed up the clustering procedure of mzclust. To this end, an agglomerative partitioning approach is used, combining measurements that are linked by values smaller than drtgap and dmzgap into single subsets. No measurements of two different subsets can be closer than drtgap and dmzgap to each other.

Value

Returns the argument MSlist, with entries made:

Parameters	MSlist[[2]]: saves the parameter settings.
Scans	MSlist[[4]]: matrix with raw measurements and tags resorted for partitions.
Partition_Index	MSlist[[5]]: Index assigning partitions to sections in the raw measurement of MSlist[[4]]; required for fast (random) access.

Imbecile

Do not set minpeak bigger than its counterpart in mzclust or mzpick. Too complicated? Then rather use enviPickwrap for adjusting all function arguments.

Warning

Despite optimized code, this function has a potential to run for a intolerable long time or out of memory if (a) the parameters are set wrongly, (b) the .mzML/.mzXML-file was not centroided or (c) the underlying data is inadequate for this peak picker. With regards to (a), do not assume gaps being larger than actually present. Instead, use plotMSlist to have a look at your data contained in MSlist after upload with readMSdata.

Author(s)

Martin Loos

See Also

mzclust,mzpart

enviPick documentation built on May 1, 2019, 8:05 p.m.