batchdataProcessing {LipidMS} | R Documentation |
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 <maialba@iislafe.es>
References
Peak-picking algorithm has been imported from enviPick R-package: https://cran.r-project.org/web/packages/enviPick/index.html
See Also
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)