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.

### 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
`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 two values, `method` - profile generation method, and `step` - profile m/z step size

### 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
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
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
retcor
  `signature(object = "xcmsSet")`: use initial grouping of peaks to do nonlinear loess retention time correction
sampclass<-
  `signature(object = "xcmsSet")`: DEPRECATED. If used, the experimental design will be replaced with a data frame with a single column matching the supplied factor.
sampclass
  `signature(object = "xcmsSet")`: get the interaction of the experimental design factors
phenoData<-
  `signature(object = "xcmsSet")`: set the `phenoData` slot
phenoData
  `signature(object = "xcmsSet")`: set the `phenoData` slot
sampnames<-
  `signature(object = "xcmsSet")`: set rownames in the `phenoData` slot
sampnames
  `signature(object = "xcmsSet")`: get rownames in the `phenoData` slot
split
  `signature("xcmsSet")`: divide into a list of objects

### Note

No notes yet.

### Author(s)

Colin A. Smith, csmith@scripps.edu

### References

A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/

### See Also

`xcmsSet`

[Package xcms version 1.16.3 Index]