xcmsSet {xcms} | R Documentation

## Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files

### Description

This function handles the construction of xcmsSet objects. It finds peaks in batch mode and pre-sorts files from subdirectories into different classes suitable for grouping.

### Usage

    xcmsSet(files = NULL, snames = NULL, sclass = NULL, phenoData = NULL,
            profmethod = "bin", profparam = list(),
            polarity = NULL, lockMassFreq=FALSE,
    	mslevel=NULL, nSlaves=0, progressCallback=NULL,
            scanrange = NULL, BPPARAM = bpparam(),
            stopOnError = TRUE, ...)

### Arguments

`files` | path names of the NetCDF/mzXML files to read
`snames` | sample names. By default the file name without extension is used.
`sclass` | sample classes.
`phenoData` | `data.frame` or `AnnotatedDataFrame` defining the sample names and classes and other sample related properties. If not provided, the argument `sclass` or the subdirectories in which the samples are stored will be used to specify sample grouping.
`profmethod` | Method to use for profile generation. Supported values are `"bin"`, `"binlin"`, `"binlinbase"` and `"intlin"` (for methods `profBin`, `profBinLin`, `profBinLinBase` and `profIntLin`, respectively). See help on `profBin` for a complete list of available methods and their supported parameters.
`profparam` | parameters to use for profile generation.
`polarity` | filter raw data for positive/negative scans
`lockMassFreq` | Performs correction for Waters LockMass function
`mslevel` | perform peak picking on data of given mslevel
`nSlaves` | DEPRECATED, use `BPPARAM` argument instead.
`progressCallback` | function to be called, when progressInfo changes (useful for GUIs)
`scanrange` | scan range to read
`BPPARAM` | a `BiocParallel` parameter object to control how and if parallel processing should be performed. Such objects can be created by the `SerialParam`, `MulticoreParam` or `SnowParam` functions.
`stopOnError` | Logical specifying whether the feature detection call should stop on the first encountered error (the default), or whether feature detection is performed in all files regardless eventual failures for individual files in which case all errors are reported as `warnings`.
`...` | further arguments to the `findPeaks` method of the `xcmsRaw` class

### Details

The default values of the `files`, `snames`, `sclass`, and `phenoData` arguments cause the function to recursively search for readable files. The filename without extention is used for the sample name. The subdirectory path is used for the sample class. If the files contain both positive and negative spectra, the polarity can be selected explicitly. The default (NULL) is to read all scans.

If `phenoData` is provided, it is stored to the `phenoData` slot of the returned `xcmsSet` class. If that `data.frame` contains a column named “class”, its content will be returned by the `sampclass` method and thus be used for the group/class assignment of the individual files (e.g. for peak grouping etc.). For more details see the help of the `xcmsSet-class`.

The step size (in m/z) to use for profile generation can be submitted either using the `profparam` argument (e.g. `profparam=list(step=0.1)`) or by submitting `step=0.1`. By specifying a value of `0` the profile matrix generation can be skipped.

The feature/peak detection algorithm can be specified with the `method` argument which defaults to the `"matchFilter"` method (`findPeaks.matchedFilter`). Possible values are returned by `getOption("BioC")$xcms$findPeaks.methods`.

The lock mass correction allows for the lock mass scan to be added back in with the last working scan. This correction gives better reproducibility between sample sets.

### Value

A `xcmsSet` object.

### Note

The arguments `profmethod` and `profparam` have no influence on the feature/peak detection. The step size parameter `step` for the profile generation in the `findPeaks.matchedFilter` peak detection algorithm can be passed using the `...`.

### Author(s)

Colin A. Smith, csmith@scripps.edu

### See Also

`xcmsSet-class`, `findPeaks`, `profStep`, `profMethod`, `profBin`, `xcmsPapply`

[Package xcms version 3.0.2 Index]