enviPick (version 1.2)

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, 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

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

• 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

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