coExpress: coExpress

In gongcongcong/mbOmic: Integrative analysis of the microbiome and metabolome

coExpress

Description

'coExpress' identify the co-expression metabolites by performing the metabolites adjant matrix basing their relative abundace. This process was mainly implemented using the WGCNA package.

Usage

coExpress(
  object,
  power = NULL,
  powerVec = seq_len(30),
  threshold = 0.8,
  message = TRUE,
  plot = FALSE,
  ...
)

Arguments

object	mbSet class
power	integer if the pickSoftThreshold function (WGCNA) can find appropriate power, this param is invalid
powerVec	vector was passed to PickST function to get the power value
threshold	numeric as the threshold to filter power value
message	logical whether to show verbose info
plot	logical whether plot in PickST function
...	additional arguments passed to WGCNA

Value

network

Author(s)

Congcong Gong

Examples

library(data.table)
path <- system.file('extdata', 'metabolites_and_genera.rda', package = 'mbOmic')
load(path)
names(genera)[1] <- 'rn'
names(metabolites)[1] <- 'rn'
b <- bSet(b = genera)
m <- mSet(m = metabolites)
res <- corr(m, b, method = 'spearman')
net <- coExpress(m, minN = 2, power = 9, message = FALSE)

gongcongcong/mbOmic documentation built on July 1, 2023, 1:47 p.m.