# 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

1 2 | ```
calcCiS(object, EIC=EIC, corval=0.75, pval=0.05, psg_list=NULL)
``` |

### Arguments

`object` |
The |

`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`

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