ProCoNA (version 1.10.0)

moduleMemberCorrelations: moduleMemberCorrelations

Description

Computes the relation between peptides and eigenvector summaries and also peptides and phenotypes.

Usage

moduleMemberCorrelations(pnet, pepdat, phenotypes)

Arguments

pnet

The peptide net object

pepdat

The peptide data matrix

phenotypes

The matrix of traits

Value

Examples

data(ProCoNA_Data)
#net1 <- buildProconaNetwork("peptide network", peptideData)
n <- length(samples(net1))
phenotypes <- matrix(rnorm(10*n), nrow=60)
pepcor <- moduleMemberCorrelations(net1, peptideData, phenotypes)

# To plot the heatmap: 
# moduleCors <- correlationWithPhenotypesHeatMap(net1, phenotypes, modules = 1:5, 
#    plot = NULL, title = "Module-trait relationships", textSize = 0.5)

#########################################################################
# quick function to write out the tables for specific modules.
#moduleData <- function(pepnet, pepcors, module, pepinfo, fileprefix) {
#  moduleX <- pepnet@peptides[which(pepnet@mergedColors==module)]
#  moduleInfo <- pepinfo[which(pepinfo$Mass_Tag_ID %in% moduleX),]
#  moduleCors <- pepcors[which(pepcors$Module==module),]
#  corname <- paste(fileprefix, "_correlations.csv", sep="")
#  write.table(moduleCors, file=corname, sep=",", row.names=F)
#  infoname <- paste(fileprefix, "_peptide_info.csv", sep="")
#  write.table(moduleInfo, file=infoname, sep=",", row.names=F)
#}
########################################################################

# WRITE OUT A TABLE WITH THE BELOW FUNCTION CALL  :)#
# moduleData(peptideNetwork, pepcor, 1, masstagdb, "Module_1")