xsAnnotate {CAMERA} | R Documentation

## xsAnnotate constructor for an provided xcmsSet object

### Description

This function deals with the construction of an xsAnnotate object. It extracts the peaktable from a provided xcmsSet, which is used for all further analysis. The xcmsSet can be a single sample or multiple sample experiment. Since some functions needs the raw data a selection algorithm must be choosen in the case of a multiple sample. CAMERA includes two different strategies: A defined selection of samples (sample = indices of samples) or the default automatic solution (sample = NA). The automatic solution chooses the best sample for a specifc groups called pseudospectrum, see groupFWHM and groupCorr. It returns a xsAnnotate object, see xsAnnotate-class.

### Usage

      xsAnnotate(xs = NULL, sample=NA, nSlaves = 1, polarity = NULL)

### Arguments

`xs` | a `xcmsSet` object
`sample` | Indices of the group xcmsSet sample, that are used for the EIC correlation step. For automatic selection don't set a value. For use all samples simply define sample = c(1:n), with n = number of samples.
`nSlaves` | For parallel mode set nSlaves higher than 1, but not higher than the number of cpu cores.
`polarity` | Set polarity mode: "positive" or "negative"

### Value

A `xsAnnotate` object.

### Author(s)

Carsten Kuhl, ckuhl@ipb-halle.de

### See Also

`xsAnnotate-class`

### Examples

     library(faahKO)
     xs <- group(faahko)
     xsa <- xsAnnotate(xs, sample=c(1:12))

     #With automatic selection
     xsa.autoselect <- xsAnnotate(xs)

[Package CAMERA version 1.48.0 Index]