View source: R/beta_div_test.R
signif_ancombc | R Documentation |
signif_ancombc(
ancombc_res,
filter_passed = TRUE,
filter_diff = TRUE,
min_abs_lfc = 0
)
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. |
This function is mainly a wrapper of the work of others.
Please make a reference to ANCOMBC::ancombc2()
if you
use this function.
A data.frame with the same number of columns than the ancombc_res
param but with less (or equal) numbers of rows
ancombc_pq()
, plot_ancombc_pq()
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)
}
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