cor.network: Correlation network analysis

In metaX: An R package for metabolomic data 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

Author(s)

Bo Wen [e-mail]

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"))

metaX documentation built on Oct. 5, 2016, 4:41 a.m.