CAMERA (version 1.28.0)

annotateDiffreport: 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

Value

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

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

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)