metaX (version 1.4.0)

cor.network: Correlation network analysis

Description

Correlation network analysis

Usage

cor.network(para, group, valueID = "value", cor.method = "spearman", threshold = 0.1, p.adjust.methods = "BH")

Arguments

para

A metaXpara object

group

Samples used for plot

valueID

The name of the column that used for plot

cor.method

Method for correlation:"pearson","spearman" or "kendall"

threshold

A threshold of significance levels of differential correlation

p.adjust.methods

c("local", holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")

...

Additional parameter

Value

The name of result file

Examples

para <- new("metaXpara")
pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
sampleListFile(para) <- sfile
para <- reSetPeaksData(para)
para <- missingValueImpute(para)
resfile <- cor.network(para,group=c("S","C"))