xcmsSet-class {xcms} | R Documentation

## Class xcmsSet, a class for preprocessing peak data

### Description

This class transforms a set of peaks from multiple LC/MS or GC/MS samples into a matrix of preprocessed data. It groups the peaks and does nonlinear retention time correction without internal standards. It fills in missing peak values from raw data. Lastly, it generates extracted ion chromatograms for ions of interest.

### Details

The `phenoData` slot (and `phenoData` parameter in the `xcmsSet` function) is intended to contain a `data.frame` describing all experimental factors, i.e. the samples along with their properties. If this `data.frame` contains a column named “class”, this will be returned by the `sampclass` method and will thus be used by all methods to determine the sample grouping/class assignment (e.g. to define the colors in various plots or for the `group` method).

The `sampclass<-` method adds or replaces the “class” column in the `phenoData` slot. If a `data.frame` is submitted to this method, the interaction of its columns will be stored into the “class” column.

Also, similar to other classes in Bioconductor, the `$` method can be used to directly access all columns in the `phenoData` slot (e.g. use `xset$name` on a `xcmsSet` object called “xset” to extract the values from a column named “name” in the `phenoData` slot).

### Objects from the Class

Objects can be created with the `xcmsSet` constructor which gathers peaks from a set NetCDF files. Objects can also be created by calls of the form `new("xcmsSet", ...)`.

### Slots

peaks

  `matrix` containing peak data.

filled

  A vector with peak indices of peaks which have been added by a `fillPeaks` method.

groups

  Matrix containing statistics about peak groups.

groupidx

  List containing indices of peaks in each group.

phenoData

  A `data.frame` containing the experimental design factors.

rt

  `list` containing two lists, `raw` and `corrected`, each containing retention times for every scan of every sample.

filepaths

  Character vector with absolute path name of each NetCDF file.

profinfo

  `list` containing the values `method` - profile generation method, and `step` - profile m/z step size and eventual additional parameters to the profile function.

dataCorrection

  `logical` vector filled if the waters Lock mass correction parameter is used.

polarity

  A string ("positive" or "negative" or NULL) describing whether only positive or negative scans have been used reading the raw data.

progressInfo

  Progress informations for some xcms functions (for GUI).

progressCallback

  Function to be called, when progressInfo changes (for GUI).

mslevel

  Numeric representing the MS level on which the peak picking was performed (by default on MS1). This slot should be accessed through its getter method `mslevel`.

scanrange

  Numeric of length 2 specifying the scan range (or `NULL` for the full range). This slot should be accessed through its getter method `scanrange`. The scan range provided in this slot represents the scans to which the whole raw data is subsetted.

.processHistory

  Internal slot to be used to keep track of performed processing steps. This slot should not be directly accessed by the user.

### Methods

c

  `signature("xcmsSet")`: combine objects together

filepaths<-

  `signature(object = "xcmsSet")`: set `filepaths` slot

filepaths

  `signature(object = "xcmsSet")`: get `filepaths` slot

diffreport

  `signature(object = "xcmsSet")`: create report of differentially regulated ions including EICs

fillPeaks

  `signature(object = "xcmsSet")`: fill in peak data for groups with missing peaks

getEIC

  `signature(object = "xcmsSet")`: get list of EICs for each sample in the set

getXcmsRaw

  `signature(object = "xcmsSet", sampleidx = 1, profmethod = profMethod(object), profstep = profStep(object), profparam=profinfo(object), mslevel = NULL, scanrange = NULL, rt=c("corrected", "raw"), BPPARAM = bpparam())`: read the raw data for one or more files in the `xcmsSet` and return it. The default parameters will apply all settings used in the original `xcmsSet` call to generate the `xcmsSet` object to be applied also to the raw data. Parameter `sampleidx` allows to specify which raw file(s) should be loaded. Argument `BPPARAM` allows to setup parallel processing.

groupidx<-

  `signature(object = "xcmsSet")`: set `groupidx` slot

groupidx

  `signature(object = "xcmsSet")`: get `groupidx` slot

groupnames

  `signature(object = "xcmsSet")`: get textual names for peak groups

groups<-

  `signature(object = "xcmsSet")`: set `groups` slot

groups

  `signature(object = "xcmsSet")`: get `groups` slot

groupval

  `signature(object = "xcmsSet")`: get matrix of values from peak data with a row for each peak group

group

  `signature(object = "xcmsSet")`: find groups of peaks across samples that share similar m/z and retention times

mslevel

  Getter method for the `mslevel` slot.

peaks<-

  `signature(object = "xcmsSet")`: set `peaks` slot

peaks

  `signature(object = "xcmsSet")`: get `peaks` slot

plotrt

  `signature(object = "xcmsSet")`: plot retention time deviation profiles

profinfo<-

  `signature(object = "xcmsSet")`: set `profinfo` slot

profinfo

  `signature(object = "xcmsSet")`: get `profinfo` slot

profMethod

  `signature(object = "xcmsSet")`: extract the method used to generate the profile matrix.

profStep

  `signature(object = "xcmsSet")`: extract the profile step used for the generation of the profile matrix.

retcor

  `signature(object = "xcmsSet")`: use initial grouping of peaks to do nonlinear loess retention time correction

sampclass<-

  `signature(object = "xcmsSet")`: Replaces the column “class” in the `phenoData` slot. See details for more information.

sampclass

  `signature(object = "xcmsSet")`: Returns the content of the column “class” from the `phenoData` slot or, if not present, the interaction of the experimental design factors (i.e. of the `phenoData` `data.frame`). See details for more information.

phenoData<-

  `signature(object = "xcmsSet")`: set the `phenoData` slot

phenoData

  `signature(object = "xcmsSet")`: get the `phenoData` slot

progressCallback<-

  `signature(object = "xcmsSet")`: set the `progressCallback` slot

progressCallback

  `signature(object = "xcmsSet")`: get the `progressCallback` slot

scanrange

  Getter method for the `scanrange` slot. See scanrange slot description above for more details.

sampnames<-

  `signature(object = "xcmsSet")`: set rownames in the `phenoData` slot

sampnames

  `signature(object = "xcmsSet")`: get rownames in the `phenoData` slot

split

  `signature("xcmsSet")`: divide the xcmsSet into a list of xcmsSet objects depending on the provided factor. Note that only peak data will be preserved, i.e. eventual peak grouping information will be lost.

`object$name`, `object$name<-value`

  Access and set `name` column in `phenoData`

`object[, i]`

  Conducts subsetting of a `xcmsSet` instance. Only subsetting on columns, i.e. samples, is supported. Subsetting is performed on all slots, also on `groups` and `groupidx`. Parameter `i` can be an integer vector, a logical vector or a character vector of sample names (matching `sampnames`).

### Author(s)

Colin A. Smith, csmith@scripps.edu, Johannes Rainer johannes.rainer@eurac.edu

### See Also

`xcmsSet`

[Package xcms version 3.16.1 Index]