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

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    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

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