Conversion of MS analysis files between several open and closed data formats.
MSFileFormats(algorithm = "pwiz", vendor = FALSE)
convertMSFiles(
files = NULL,
outPath = NULL,
dirs = TRUE,
anaInfo = NULL,
from = NULL,
to = "mzML",
overWrite = FALSE,
algorithm = "pwiz",
centroid = algorithm != "openms",
filters = NULL,
extraOpts = NULL,
PWizBatchSize = 1
)Either "pwiz" (implemented by msConvert of
ProteoWizard), "openms" (implemented by FileConverter of
OpenMS) or "bruker" (implemented by DataAnalysis).
If TRUE only vendor formats are returned.
The files argument should be a character
vector with input files. If files contains directories and
dirs=TRUE then files from these directories are also considered. An
alternative method to specify input files is by the anaInfo
argument. If the latter is specified files may be NULL.
A character vector specifying directories that should be used
for the output. Will be re-cycled if necessary. If NULL, output
directories will be kept the same as the input directories.
An analysis info table used to
retrieve input files. Either this argument or files (or both) should
be set (i.e. not NULL).
Input format (see below). These are used to find analyses when
dirs=TRUE or anaInfo is set.
Output format: "mzXML" or "mzML".
Should existing destination file be overwritten
(TRUE) or not (FALSE)?
Set to TRUE to enable centroiding (not supported if
algorithm="openms"). In addition, when algorithm="pwiz" the
value may be "vendor" to perform centroiding with the vendor
algorithm or "cwt" to use ProteoWizard's wavelet algorithm.
When algorithm="pwiz": a character vector
specifying one or more filters. The elements of the specified vector are
directly passed to the --filter option (see
here)
A character vector specifying any extra commandline
parameters passed to msConvert or FileConverter. Set to
NULL to ignore. For options: see
FileConverter
and
msConvert.
When algorithm="pwiz": the number of analyses to
process by a single call to msConvert. Usually a value of one is
most efficient. Set to zero to run all analyses all at once from a single
call.
MSFileFormats returns a character with all supported
input formats (see below).
convertMSFiles converts the data format of an analysis to
another. It uses tools from
ProteoWizard
(msConvert command), OpenMS
(FileConverter command) or Bruker DataAnalysis to perform the
conversion. Supported input and output formats include mzXML,
.mzML and several vendor formats, depending on which algorithm is
used.
convertMSFiles (except if algorithm="bruker") uses multiprocessing to parallelize
computations. Please see the parallelization section in the handbook for
more details and patRoon options for configuration
options.
Possible output formats (to argument) are
mzXML and mzML.
Possible input formats (from argument) depend on the algorithm that
was chosen and may include:
thermo: Thermo .RAW files (only
algorithm="pwiz").
bruker: Bruker .d, .yep, .baf and
.fid files (only algorithm="pwiz" or
algorithm="bruker").
agilent: Agilent .d files (only
algorithm="pwiz").
ab: AB Sciex .wiff files (only
algorithm="pwiz").
waters Waters .RAW files (only
algorithm="pwiz").
mzXML/mzML: Open format .mzXML/.mzML
files (only algorithm="pwiz" or algorithm="openms").
Note that the actual supported file formats of ProteoWizard depend on how it was installed (see here).
Rst2016patRoon
Chambers2012patRoon
if (FALSE) { # \dontrun{
# Use FileConverter of OpenMS to convert between open mzXML/mzML format
convertMSFiles("standard-1.mzXML", to = "mzML", algorithm = "openms")
# Convert all Thermo .RAW files in the analyses/raw directory to mzML and
# store the files in analyses/mzml. During conversion files are centroided by
# the peakPicking filter and only MS 1 data is kept.
convertMSFiles("analyses/raw", "analyses/mzml", dirs = TRUE, from = "thermo",
centroid = "vendor", filters = "msLevel 1")
} # }