calcCiS-methods {CAMERA} | R Documentation

## Calculate peak distance matrix after EIC correlation

### Description

Processing an xsAnnotate object and correlates peak EIC curves from one pseudospectrum, using a precalculated EIC matrix (`getAllPeakEICs`). It return a weighted edge list as distance matrix between peaks according to the correlation analysis. The edge value is the pearson correlation coefficent. The list can be used as input for `calcPC`.

### Usage

        calcCiS(object, EIC=EIC, corval=0.75, pval=0.05, psg_list=NULL)

### Arguments

`object` | The `xsAnnotate` object
`EIC` | EIC Matrix
`corval` | Correlation threshold for the EIC correlation
`pval` | pvalue for testing correlation of significance
`psg_list` | Vector of pseudospectra indices. The correlation analysis will be only done for those groups

### Details

The algorithm correlates the EIC of a every peak with all others, to find the peaks that belong to one substance. LC/MS data should grouped with groupFWHM first. This step reduce the runtime a lot and increased the number of correct classifications. Only correlation with a higher value than the correlation threshold and significant p-values will be returned.

### Value

A matrix with 4 columns:

`x` | peak index
`y` | peak index
`cor` | correlation value
`ps` | pseudospectrum index, which contains x and y

### Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

### See Also

`calcCaS` `groupCorr` `getAllPeakEICs` `xsAnnotate-class`

[Package CAMERA version 1.40.0 Index]