annotateDiffreport {CAMERA} | R Documentation

## Automatic deconvolution/annotation of LC/ESI-MS data

### Description

Wrapper function for the xcms diffreport and the annotate function. Returns a diffreport within the annotation results.

### Usage

    annotateDiffreport(object, sample=NA, nSlaves=1, sigma=6, perfwhm=0.6,
      cor_eic_th=0.75, cor_exp_th = 0.75, graphMethod="hcs", pval=0.05, calcCiS=TRUE,
      calcIso=FALSE, calcCaS=FALSE, maxcharge=3, maxiso=4, minfrac=0.5,
      ppm=5, mzabs=0.015, quick=FALSE, psg_list=NULL, rules=NULL,
      polarity="positive", multiplier=3, max_peaks=100, intval="into",
      pval_th = NULL, fc_th = NULL, sortpval=TRUE, ...)

### Arguments

`object` | xcmsSet with peak group assignments
`sample` | xsAnnotate: Sample selection for grouped xcmsSet, see xsAnnotate-class
`nSlaves` | xsAnnotate: Use parallel CAMERA mode, require Rmpi
`sigma` | groupFWHM: multiplier of the standard deviation
`perfwhm` | groupFWHM: percentage of FWHM width
`cor_eic_th` | groupCorr: Correlation threshold for EIC correlation (0..1)
`cor_exp_th` | groupCorr: Threshold for intensity correlations across samples (0..1)
`graphMethod` | groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra
`pval` | groupCorr: significant correlation threshold
`calcCiS` | groupCorr: Use correlation inside samples for peak grouping
`calcIso` | groupCorr: Use isotopic relationship for peak grouping
`calcCaS` | groupCorr: Use correlation across samples for peak grouping
`maxcharge` | findIsotopes: max. ion charge
`maxiso` | findIsotopes: max. number of expected isotopes
`minfrac` | findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation
`ppm` | General ppm error
`mzabs` | General absolut error in m/z
`quick` | Use only groupFWHM and findIsotopes
`psg_list` | Calculation will only be done for the selected groups
`rules` | findAdducts: User defined ruleset
`polarity` | findAdducts: Which polarity mode was used for measuring of the ms sample
`multiplier` | findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions
`max_peaks` | How much peaks will be calculated in every thread using the parallel mode
`intval` | General used intensity value (into, maxo, intb)
`pval_th` | pval threshold. Creates a new psg_list. A pseudospectra is selected if it contains peaks, with pval < pval_th
`fc_th` | Same as pval. Select those groups with contains peaks with fold-change > fc_th. Pval_th and fc_th can be combined
`sortpval` | Sort diffreport after pvalues
`...` | Diffreport parameters see diffreport

### Details

Batch script wrapper for combining the annotation and the diffreport for a (grouped) xcmsSet `xs`. Function list: 1: diffreport(), 2: groupFWHM(), 3: findIsotopes(), 4: groupCorr(), 5: findAdducts() For a speedup calculation users can create a quick run, with quick = TRUE to preselect pseudospectra of interest. The indices of those pseudospectra are set with psg_list in a second run. On the other hand, a automatic selection with pval_th and/or fc_th can be performed. Returns the normal xcms diffreport table, with the additional CAMERA slots

### Value

`annotateDiffreport` returns an diffreport, see diffreport, within additional columns containing the annotation results.

### Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

### Examples

     #Multiple sample
     library(CAMERA)
     library(faahKO)
     xs.grp     <- group(faahko)
     xs.fill    <- fillPeaks(xs.grp)

     #fast preselection
    # diffreport  <- annotateDiffreport(xs.fill,quick=TRUE)
    # index <- c(1,18,35,45,56) #Make only for those grps a adduct annotation
    # diffreport2 <- annotateDiffreport(xs.fill,psg_list=index,metlin = TRUE)

     #automatic selection for groups with peaks p-val < 0.05 and fold-change > 3
    # diffreport <- annotateDiffreport(xs.fill,pval_th=0.05,fc=3)

[Package CAMERA version 1.36.0 Index]