Welcome to the fetch repository on GitHub!
fetch is built on the ALDEx2 package but also allows for global test statistics to be computed. These test statistics can be used to determine which features should be tested on a taxa by taxa basis.
To run fetch with one condition:
library(fetch)
data(selex)
#subset for efficiency
selex <- selex[1201:1600,]
conds <- c(rep("NS", 7), rep("S", 7))
f <- fetch(selex, conds, mc.samples=10, denom="all", test = "global")
f
To run fetch with more than one condition:
data(selex)
#subset for efficiency
selex <- selex[1201:1600,]
covariates <- data.frame("A" = sample(0:1, 14, replace = TRUE),
"B" = c(rep(0, 7), rep(1, 7)))
mm <- model.matrix(~ A + B, covariates)
f <- fetch(selex, mm, mc.samples=10, denom="all", test = "global")
f