enviPickwrap: Peak detection for LC-HRMS .mzML and .mzXML data
In enviPick: Peak Picking for High Resolution Mass Spectrometry Data

Description Usage Arguments Details Value Author(s) See Also

A wrapper combining data upload, partitioning, EIC clustering and EIC peak detection from readMSdata, mzagglom, mzclust and mzpick.

enviPickwrap(filepath.mzXML, MSlevel=c(1), dmzgap=15, dmzdens=4, ppm=TRUE, 
drtgap=500, drtsmall=20, drtdens=250, drtfill=10, drttotal=200, minpeak=4,  
recurs=3, weight=2, SB=3, SN=2, minint=1E5, maxint=1E7, ended=2, 
ion_mode=FALSE, progbar=FALSE)

`filepath.mzXML`	Path to the .mzXML file to be read, `readMSdata`
`MSlevel`	numeric 1 (MS) or 2 (MS-MS), `readMSdata`
`dmzgap`	m/z gap width for partitioning, `mzpart`
`dmzdens`	Maximum measurement deviation (+/-) of m/z within an EIC, `mzclust`
`ppm`	`dmzgap`, given in ppm (TRUE) or as absolute value (FALSE)
`drtgap`	RT gap width for partitioning, `mzpart`
`drtsmall`	Peak definition - RT window of a peak; cp. `minpeak` argument
`drtdens`	Maximum length of EICs, `mzclust`
`drtfill`	RT gap length to be filled, `mzpick`
`drttotal`	Maximum RT length of a single peak, `mzpick`
`minpeak`	Peak definition - minimum number of measurements per peak to found in windows of `drtsmall` and `dmzsmall`, `mzpick`
`recurs`	Maximum number of peaks within one EIC, `mzpick`
`weight`	Weight for assigning measurements to a peak, `mzpick`
`SB`	Signal-to-base ratio, `mzpick`
`SN`	Signal-to-noise ratio, `mzpick`
`minint`	Minimum intensity of a peak, `mzpick`
`maxint`	Peaks above this intensity are alwas included, regardless of checks for `SB` or `SN`,`mzpick`
`ended`	Within the peak detection recursion set by argument `recurs`, how often can a peak detection fail, to end the recursion? `mzpick`
`ion_mode`	"positive" or "negative" ionization. Otherwise set to FALSE, see details.
`progbar`	Show a progress bar (TRUE or FALSE)? May only work under Windows OS.

For further details on the parameter settings, please refer to the arguments of the underlying functions readMSdata, mzagglom, mzclust and mzpick. ion_mode allows to filter scans of a specific polarity from .mzXML files, if not set to FALSE; useful for files acquired under polarity switching.

MSlist

`State`	MSlist[[1]]: tags the individual steps the MSlist has undergone for peak picking.
`Parameters`	MSlist[[2]]: saves the parameter settings.
`Results`	MSlist[[3]]: saves the result summary values
`Scans`	MSlist[[4]]: matrix with raw measurements (m/z, intensity, RT) and tags for partitions, EIC cluster or individual peaks.
`Partition_Index`	MSlist[[5]]: Index assigning partitions to sections in the raw measurment of MSlist[[4]]. Required for fast (random) access, e.g., plotting.
`EIC_index`	MSlist[[6]]: Index assigning EIC clusters to sections in the raw measurment of MSlist[[4]]. Required for fast access.
`Peak_index`	MSlist[[7]]: Index assigning picked peaks to sections in the raw measurment of MSlist[[4]]. Required for fast access.
`Peaklist`	MSlist[[8]]: Final peak list, cp. `mzpick`