LipidMS (version 0.1.0)

dataProcessing: Process mzXML files: peakpicking and deisotoping

Description

Process mzXML files: peak-picking using enviPick and deisotoping using CAMERA.

Usage

dataProcessing(file, msLevel, polarity, dmzgap = 50, drtgap = 25,
  ppm = TRUE, minpeak, maxint = 1e+09, dmzdens, drtdens = 20,
  merged = FALSE, drtsmall, drtfill = 20, drttotal = 200, recurs = 4,
  weight, SB, SN = 2, minint, ended = 2, progbar = FALSE, from = FALSE,
  to = FALSE)

Arguments

file

path of the mzXML input file

msLevel

numeric value indicating if data belongs to level 1 (fullMS) or level 2 (MS/MS)

polarity

character value: negative or positive

dmzgap

enviPick parameter. 50 by default.

drtgap

enviPick parameter. 25 by default.

ppm

enviPick parameter. TRUE by default.

minpeak

enviPick parameter. Optional. By default, 5 when msLevel = 1 and 4 when msLevel = 2.

maxint

enviPick parameter. 1E9 by default.

dmzdens

enviPick parameter. Optional. By default, 15 when msLevel = 1 and 20 when msLevel = 2.

drtdens

enviPick parameter. Optional. 20 by default.

merged

enviPick parameter. FALSE by default.

drtsmall

enviPick parameter. Optional. By default, 100 when msLevel = 1 and 20 when msLevel = 2.

drtfill

enviPick parameter. 20 by default.

drttotal

enviPick parameter. 200 by default.

recurs

enviPick parameter. 4 by default.

weight

enviPick parameter. Optional. By default, 1 when msLevel = 1 and 2 when msLevel = 2.

SB

enviPick parameter. Optional. By default, 3 when msLevel = 1 and 2 when msLevel = 2.

SN

enviPick parameter. 2 by default.

minint

enviPick parameter. Optional. By default, 1000 when msLevel = 1 and 100 when msLevel = 2.

ended

enviPick parameter. 2 by default.

progbar

enviPick parameter. FALSE by default.

from

enviPick parameter. FALSE by default.

to

enviPick parameter. FALSE by default.

Value

Data frame with 3 columns (m.z, RT and int) containing the peaklist.

Details

This function executes 2 steps: 1) peak-picking using enviPick package and 2) it removes isotopes using CAMERA. If msLevel = 1, only ions with more than 1 isotope are kept.

References

https://cran.r-project.org/web/packages/enviPick/index.html

Kuhl C, Tautenhahn R, Boettcher C, Larson TR ans Neumann S (2012). "CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography-mass spectrometry data sets." Analytical Chemistry, 84, pp. 283-289. htto://pubs.acs.org/doi/abs/10.1021/ac202450g.

Examples

# NOT RUN {
# }
# NOT RUN {
dataProcessing("input_file.mzXML", msLevel = 1, polarity = "positive")
# }
# NOT RUN {
# }