enviPick (version 1.5)

enviPickbatch: Batch peak picking for several .mzXML input files

Description

Given a folder of .mzXML input files and subsequent processing, .csv peak tables with picked peaks are written to an output folder

Usage

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

Arguments

folderin

Folder containing .mzXML input files

folderout

Destination folder for .csv peak tables

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.

Value

Folder with .csv peak tables, each containing columns with: m/z (mean m/z of peak measurements), var_m/z (m/z variation of peak measurements), max_int (base-line corrected maximum intensity), sum_int (sum of all base-line corrected peak measurement intensities), RT (retention time at maximum intensity), minRT (start peak RT), maxRT (end peak RT), peak# (peak ID number), EIC# (EIC ID number), Score (not yet implemented)

Details

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.

See Also

readMSdata mzagglom mzclust mzpick plotMSlist