enviPickwrap: Peak detection for LC-HRMS .mzML and .mzXML data

Description

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

Usage

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)

Arguments

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

Signal-to-base ratio, mzpick

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

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

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.

Description

Usage

Arguments

Value

Details

See Also