CAMERA (version 1.28.0)

calcCaS-methods: 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.

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

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.

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)