annotateDiffreport: Automatic deconvolution/annotation of LC/ESI-MS data

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

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 <[e-mail]>

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)

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.