getCorrAdjacency: compute correlation coefficients, pvalues and directions

In kwanjeeraw/grinn: graph database and R package for omics data integration

Description

compute correlation coefficients, pvalues and relation directions from normalized data using WGCNA::cor and WGCNA::corPvalueStudent to return outputs for further uses by fetchCorrNetwork, fetchDiffCorrNetwork. datX and datY are matrices in which rows are samples and columns are entities, require the first row to specify entity types e.g. metabolite. If datY is given, then the correlations between the columns of datX and the columns of datY are computed. Otherwise the correlations of the columns of datX are computed.

Usage

getCorrAdjacency(datX, datY, method)

References

Langfelder P. and Horvath S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9:559

Dudoit S., Yang YH., Callow MJ. and Speed TP. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments, STATISTICA SINICA, 12:111

Langfelder P. and Horvath S. Tutorials for the WGCNA package http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html

See Also

cor, corPvalueStudent, fetchCorrNetwork, fetchDiffCorrNetwork datMet = read.delim("~/grinn_sample/Lung_MET.txt", header=TRUE, stringsAsFactors=FALSE) datPrt = read.delim("~/grinn_sample/Lung_PRT.txt", header=TRUE, stringsAsFactors=FALSE) Convert kegg ids to grinn ids grinnID = convertToGrinnID(txtInput=datMet$KEGG.id, nodetype="metabolite", dbXref="kegg") grinnID = grinnID[!duplicated(grinnID[,1]),] #keep the first mapped id internal function, called by apply for formatting ids mapToInput = function(x) id = which(grinnID$FROM_kegg == x[2]) out = ifelse(length(id)>0,as.character(grinnID$GRINNID[id]),x[1]) formatting input data datMet = t(datMet) colnames(datMet) = apply(datMet,2,mapToInput) datMet = datMet[-c(1,2),] formatting input data datPrt = t(datPrt) colnames(datPrt) = datPrt[1,] datPrt = datPrt[-1,] corAdj = getCorrAdjacency(datX=datMet, datY=datPrt, method="spearman")

kwanjeeraw/grinn documentation built on May 20, 2019, 7:07 p.m.