enviPick (version 1.2)

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, 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

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.

See Also

readMSdata mzagglom mzclust mzpick plotMSlist