(i) For Agilent Technologies providers (using the default parameters): each analysis returns a folder. The input files in the sample folder can be of different origins: D folder is created and contains different files from the chromatograph and from the mass spectrometer. It allows recovering temporary informations if the function stopped before ending because of errors.ĭetails After a GC-MS analysis with Agilent apparatus, a. If quant =TRUE for DataType = Agilent, two supplementary columns corrArea and PercTot are added after the column retention time.Ī temporary list is generated during the process. It contains one row per peak and per individual with the information in column of the sample name, the retention time (or retention index) and the relative mass spectrum. MS.DataCreationCDF returns a data matrix as an object in R and this data matrix, called initial_DATA.txt, is also saved in folder Output_MSDataCreation_resultdate_time.TRUE indicates that the two quantification columns corr.area (corrected peak area) and Value The option quant indicates if quantification information should be extracted from rteres.txt and added to the initial data matrix.

MS.DataCreationCDF(path, pathCDF='', mz, apex, quant = FALSE) Arguments If the input file is in Agilent format, it is possible to add quantification information by reporting percent of the total corrected area and corrected area. Each row of the output data matrix represent one peak in one analysis and give the sample name in first column, the peak retention time (or retention index) in second column and the mass spectrum of the peak in the following columns. For all input files, peak retention times (or retention indices) are retrieved from the chromatograms (from rteres.txt file) and associated to their respective mass spectrum (from CDF file). Description This function constructs an initial data matrix by collecting and assembling the information from chromatograms and mass spectra from several GC-MS analyses. Warning: the use of xcms package is necessary. MS.DataCreationCDF: Same as MS.DataCreation but with the capability to read AIA/ANDI NetCDF, mzXML, mzData and mzML files.Ĭreate an initial data matrix from GC-MS analyses by collecting and assembling the information from chromatograms and mass spectra from AIA/ANDI NetCDF, mzXML, mzData and mzML files.

Aia .cdf files