calcCiS-methods: Calculate peak distance matrix after EIC correlation

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

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 <[e-mail]>

See Also

calcCaS groupCorr getAllPeakEICs xsAnnotate-class

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.