calcCaS-methods {CAMERA} | R Documentation

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

### Description

Calculate the correlation across samples. Filtering correlation with specific parameters and returns a correlation matrix.

### Usage

      calcCaS(object,corval=0.75, pval=0.05, intval="into")

### Arguments

`object` | The `xsAnnotate` object
`corval` | Correlation threshold for positive hits
`pval` | P-Value threshold for significance level of correlation
`intval` | Selection of the intensity values that should be used in the correlation analysis. Can be into, maxo or intb.

### Details

Calculate pearson correlation between the peak intensites over all samples. Afterwards use cor.test for returning only significant correlation. Returns only those correlation, which are above both threshold. Set corval and pval to 0 to get the unfiltered correlation matrix. If the object is pregrouped with groupFWHM, then the correlation is only calculated between peaks within a pseudospectrum. Otherwise between all peaks.

### Value

A matrix with 4 columns:

`x` | peak index according to peaktable
`y` | peak index according to peaktable
`cor` | correlation value between peak x and peak y
`ps` | pseudospektrum index for both peaks

### Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

### See Also

`calcCiS` `groupCorr` `xsAnnotate-class`

### Examples

     library(CAMERA)
     #Multiple sample
     library(faahKO)
     xs.grp       <- group(faahko)
     #create xsAnnotate object
     xsa          <- xsAnnotate(xs.grp)
     #generate pseudospectra
     xsa.group    <- groupFWHM(xsa)
     #calculate correlation
     correlationMatrix <- calcCaS(xsa.group)

[Package CAMERA version 1.42.0 Index]