ESI-MS data
In CAMERA: Collection of annotation related methods for mass spectrometry data

Description Usage Arguments Details Value Author(s) Examples

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

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, ...)

`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

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

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

Carsten Kuhl <ckuhl@ipb-halle.de>

 #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)