batchdataProcessing: Process several mzXML files (peakpicking and isotope...

In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

Process several mzXML files (peakpicking and isotope annotation) and create an msbatch for batch processing.

Description

Process several mzXML files (peakpicking and isotope annotation) and create an msbatch for batch processing.

Usage

batchdataProcessing(
  files,
  metadata,
  polarity,
  dmzagglom = 15,
  drtagglom = 500,
  drtclust = 100,
  minpeak = c(5, 3),
  drtgap = 10,
  drtminpeak = 15,
  drtmaxpeak = c(100, 200),
  recurs = 5,
  sb = c(3, 2),
  sn = 2,
  minint = c(1000, 100),
  weight = c(2, 3),
  dmzIso = 10,
  drtIso = 5,
  parallel = FALSE,
  ncores,
  verbose = TRUE
)

Arguments

files	file paths of the mzXML files. Optional.
metadata	csv file or data.frame with 3 columns: sample (samples named as the mzXML files), acquisitionmode (MS, DIA or DDA) and groups (i.e. blank, QC, sample). DIA, DDA and MS files are allowed, but only DIA and DDA files will be used for lipid annotation.
polarity	character value: negative or positive.
dmzagglom	mz tolerance (in ppm) used for partitioning and clustering.
drtagglom	rt window used for partitioning (in seconds).
drtclust	rt window used for clustering (in seconds).
minpeak	minimum number of measurements required for a peak.
drtgap	maximum RT gap length to be filled (in seconds).
drtminpeak	minimum RT width of a peak (in seconds). At least minpeak within the drtminpeak window are required to define a peak.
drtmaxpeak	maximum RT width of a single peak (in seconds).
recurs	maximum number of peaks within one EIC.
sb	signal-to-base ratio.
sn	signal-to-noise ratio.
minint	minimum intensity of a peak.
weight	weight for assigning measurements to a peak.
dmzIso	mass tolerance for isotope matching.
drtIso	time windows for isotope matching.
parallel	logical.
ncores	number of cores to be used in case parallel is TRUE.
verbose	print information messages.

Details

This function executes 2 steps: 1) creates an msobject for each sample (using the dataProcessing function) and 2) sets an msbatch (setmsbatch function).

Numeric arguments accept one or two values for MS1 and MS2, respectively.

Value

msbatch

Author(s)

M Isabel Alcoriza-Balaguer <[e-mail]>

References

Peak-picking algorithm has been imported from enviPick R-package: https://cran.r-project.org/web/packages/enviPick/index.html

See Also

dataProcessing and setmsbatch

Examples

## Not run: 
# if metadata is a data frame:
msbatch <- batchdataProcessing(metadata$sample, metadata, polarity = "positive",
dmzagglom = 25, drtagglom = 500, drtclust = 60, minpeak = c(5, 3),
drtgap = 5, drtminpeak = 20, drtmaxpeak = 100, recurs = 5, sb = c(3, 2),
sn = 2, minint = c(1000, 100), weight = 2, dmzIso = 10, drtIso = 5)

# if metadata is a csv file:
msbatch <- batchdataProcessing(metadata = "metadata.csv", polarity = "positive",
dmzagglom = 25, drtagglom = 500, drtclust = 60, minpeak = c(5, 3),
drtgap = 5, drtminpeak = 20, drtmaxpeak = 100, recurs = 5, sb = c(3, 2),
sn = 2, minint = c(1000, 100), weight = 2, dmzIso = 10, drtIso = 5)

## End(Not run)

LipidMS documentation built on May 29, 2024, 11:24 a.m.