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mcalgaro93 / benchdamic

Benchmark of differential abundance methods on microbiome data
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DA_ALDEx2 #7

Closed bylam closed 1 month ago

bylam commented 5 months ago

how to save the result DA_ALDEx2,. It seems that the results only include values such as we.ep and we.eBH, but do not provide the final result of the enriched group.

mcalgaro93 commented 5 months ago

Dear @bylam. You should be able to find the whole ALDEx2 output on the statInfo slot of every output related to ALDEx2.

Here is an example:

library(benchdamic)
library(phyloseq)
set.seed(1)
# Create a very simple phyloseq object
counts <- matrix(rnbinom(n = 300, size = 3, prob = 0.5), nrow = 50, ncol = 6)
metadata <- data.frame("Sample" = c("S1", "S2", "S3", "S4", "S5", "S6"),
                       "group" = as.factor(c("A", "A", "A", "B", "B", "B")))
ps <- phyloseq::phyloseq(phyloseq::otu_table(counts, taxa_are_rows = TRUE),
                         phyloseq::sample_data(metadata))
# Differential abundance with wilcox test and denom = "iqlr"
DA_w <- DA_ALDEx2(ps, design = "group", test = "wilcox", denom = "iqlr", 
    paired.test = FALSE, contrast = c("group", "B", "A"))

head(DA_t$statInfo)

The effect column contains the direction of the differential abundance.

Please, let me know if this answers your question. Matteo