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Filter ancombc_pq results

Source: R/beta_div_test.R
signif_ancombc.Rd

lifecycle-experimental

Internally used in plot_ancombc_pq().

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.

Value

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

Details

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

See also

ancombc_pq(), plot_ancombc_pq()

Examples

# \donttest{
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)
}
#> Warning: The group variable has < 3 categories 
#> The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated
#> Warning: The number of taxa used for estimating sample-specific biases is: 9
#> A large number of taxa (>50) is required for the consistent estimation of biases
#> Obtaining initial estimates ...
#> Estimating sample-specific biases ...
#> Warning: Estimation of sampling fractions failed for the following samples:
#> BT-006-M_S55_MERGED.fastq.gz, C21-NV1-B_S62_MERGED.fastq.gz, CB8-019-H_S70_MERGED.fastq.gz, DY5-004-B_S96_MERGED.fastq.gz, DY5-004-H_S97_MERGED.fastq.gz, J18-004-M_S116_MERGED.fastq.gz, W26-001-B_S165_MERGED.fastq.gz, X24-009-B_S170_MERGED.fastq.gz
#> These samples may have an excessive number of zero values
#> Sensitivity analysis for pseudo-count addition to 0s: ...
#> ANCOM-BC2 primary results ...
#>  [1] taxon                 lfc_(Intercept)       lfc_Time15           
#>  [4] se_(Intercept)        se_Time15             W_(Intercept)        
#>  [7] W_Time15              p_(Intercept)         p_Time15             
#> [10] q_(Intercept)         q_Time15              diff_(Intercept)     
#> [13] diff_Time15           passed_ss_(Intercept) passed_ss_Time15     
#> <0 rows> (or 0-length row.names)
# }