signif_ancombc: Filter ancombc_pq results

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Filter ancombc_pq results

Description

Usage

signif_ancombc(
  ancombc_res,
  filter_passed = TRUE,
  filter_diff = TRUE,
  min_abs_lfc = 0
)

Arguments

ancombc_res	(required) the result of the ancombc_pq function For the moment only bimodal factors are possible.
filter_passed	(logical, default TRUE) Do we filter using the column passed_ss? The passed_ss value is TRUE if the taxon passed the sensitivity analysis, i.e., adding different pseudo-counts to 0s would not change the results.
filter_diff	(logical, default TRUE) Do we filter using the column diff? The diff value is TRUE if the taxon is significant (has q less than alpha)
min_abs_lfc	(integer, default0) Minimum absolute value to filter results based on Log Fold Change. For ex. a value of 1 filter out taxa for which the abundance in a given level of the modality is not at least the double of the abundance in the other level.

Details

This function is mainly a wrapper of the work of others. Please make a reference to ANCOMBC::ancombc2() if you use this function.

Value

A data.frame with the same number of columns than the ancombc_res param but with less (or equal) numbers of rows

See Also

ancombc_pq(), plot_ancombc_pq()

Examples

if (requireNamespace("mia")) {
  data_fungi_mini@tax_table <- phyloseq::tax_table(cbind(
    data_fungi_mini@tax_table,
    "taxon" = taxa_names(data_fungi_mini)
  ))

  res_time <- ancombc_pq(
    data_fungi_mini,
    fact = "Time",
    levels_fact = c("0", "15"),
    tax_level = "taxon",
    verbose = TRUE
  )

  signif_ancombc(res_time)
}

MiscMetabar documentation built on May 29, 2024, 10:39 a.m.