groupCorr {CAMERA} | R Documentation

## EIC correlation grouping of LC/ESI-MS data

### Description

Peak grouping after correlation information into pseudospectrum groups for an xsAnnotate object. Return an xsAnnotate object with grouping information.

### Usage

      groupCorr(object,cor_eic_th=0.75, pval=0.05, graphMethod="hcs",
      calcIso = FALSE, calcCiS = TRUE, calcCaS = FALSE, psg_list=NULL, xraw=NULL,
      cor_exp_th=0.75, intval="into", ...)

### Arguments

`object` | The `xsAnnotate` object
`cor_eic_th` | Correlation threshold for EIC correlation
`pval` | p-value threshold for testing correlation of significance
`graphMethod` | Clustering method for resulting correlation graph. See calcPC for more details.
`calcIso` | Include isotope detection informationen for graph clustering
`calcCiS` | Calculate correlation inside samples
`calcCaS` | Calculate correlation accross samples
`psg_list` | Vector of pseudospectra indices. The correlation analysis will be only done for those groups
`xraw` | Optional xcmsRaw object, which should be used for raw data extraction
`cor_exp_th` | Threshold for intensity correlations across samples
`intval` | Selection of the intensity values (such as "into") that should be used in the correlation analysis. See `getPeaklist` for all allowed values.
`...` | Additional parameter

### Details

The algorithm calculates different informations for group peaks into so called pseudospectra. This pseudospectra contains peaks, with have a high correlation between each other. So far three different kind of information are available. Correlation of intensities across samples (need more than 3 samples), EIC correlation between peaks inside a sample and additional the informationen about recognized isotope cluster can be included. After calculation of all these informations, they are combined as edge value into a graph object. A following graph clustering algorithm separate the peaks (nodes in the graph) into the pseudospectra.

### Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

### See Also

`calcCiS` `calcCaS` `calcPC` `xsAnnotate-class`

### Examples

     library(CAMERA)
     file        <- system.file('mzdata/MM14.mzdata', package = "CAMERA");
     xs          <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5, 10));
     an          <- xsAnnotate(xs);
     an.group    <- groupFWHM(an);
     an.iso      <- findIsotopes(an.group); #optional step for using isotope information
     an.grp.corr <- groupCorr(an.iso, calcIso=TRUE);

     #For csv output
     # write.csv(file="peaklist_with_isotopes.csv",getPeaklist(an))

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

     #With selected sample
     xsa          <- xsAnnotate(xs.grp, sample=1)
     xsa.group    <- groupFWHM(xsa)
     xsa.iso      <- findIsotopes(xsa.group) #optional step
     xsa.grp.corr <- groupCorr(xsa.iso, calcIso=TRUE)

     #With automatic selection
     xsa.auto     <- xsAnnotate(xs.grp)
     xsa.grp      <- groupFWHM(xsa.auto)
     xsa.iso      <- findIsotopes(xsa.grp) #optional step
     index        <- c(1,4) #Only group one and four will be calculate
     #We use also correlation across sample
     xsa.grp.corr <- groupCorr(xsa.iso, psg_list=index, calcIso=TRUE, calcCaS=TRUE)
     #Note: Group 1 and 4 have no subgroups

[Package CAMERA version 1.48.0 Index]