ALDEx2 analysis on each phyloseq object in a list_phyloseq

Performs ALDEx2 differential abundance analysis using MiscMetabar::aldex_pq() on each phyloseq object in a list_phyloseq and returns a combined result table.

Usage

aldex_lpq(x, bifactor, modalities = NULL, gamma = 0.5, verbose = TRUE, ...)

Arguments

x

(required) A list_phyloseq object.

bifactor

(character, required) The name of a dichotomous column in sample_data to use as the grouping factor. Must be present in all phyloseq objects.

modalities

(character vector, default NULL) Two modalities of bifactor to compare. If NULL, uses the two levels present in the data.

gamma

(numeric, default 0.5) The gamma parameter for ALDEx2.

verbose

(logical, default TRUE) If TRUE, print progress messages.

...

Additional arguments passed to MiscMetabar::aldex_pq().

Value

A tibble with the combined ALDEx2 results from all phyloseq objects. Each row corresponds to one taxon in one phyloseq object, with columns from ALDEx2 output plus taxon (from rownames) and name (identifying the source phyloseq object).

Details

This function requires that the list_phyloseq type is NOT SEPARATE_ANALYSIS, as the bifactor must be common across all phyloseq objects.

When no common taxa exist across the phyloseq objects, taxa names are suffixed with the phyloseq object name to make them distinguishable.

See also

MiscMetabar::aldex_pq(), ancombc_lpq(), multipatt_lpq()

Examples

if (FALSE) { # \dontrun{
lpq <- list_phyloseq(
  list(
    fungi = data_fungi,
    fungi_clust = postcluster_pq(data_fungi)
  ),
  same_bioinfo_pipeline = FALSE
)

results <- aldex_lpq(lpq,
  bifactor = "Height",
  modalities = c("Low", "High")
)
results

ALDEx2::aldex.plot(filter(results, name == "fungi"), type = "volcano")
ALDEx2::aldex.plot(filter(results, name == "fungi_clust"), type = "volcano")

ggplot(results, aes(y = taxon, x = effect, col = wi.eBH)) +
  geom_point()
} # }