coExpress | R Documentation |
'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.
coExpress( object, power = NULL, powerVec = seq_len(30), threshold = 0.8, message = TRUE, plot = FALSE, ... )
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 |
network
Congcong Gong
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)
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