createTaxonTable.RdCreate a table of most frequent taxa in a data.frame
createTaxonTable(dat, n = 10)data.frame produced by importBugSigDB, subsetted as desired
number of taxa to return (if sig.type=="both", this is the number of taxa to return for each direction)
kable table with increased and decreased taxa and a binomial test based on total number of studies in the data.frame
full.dat <- bugsigdbr::importBugSigDB()
#> Using cached version from 2025-05-05 19:21:34
createTaxonTable(full.dat, n=20)
#> # A tibble: 20 × 15
#> `Taxon Name` `Taxonomic Level` total_signatures increased_signatures
#> <chr> <chr> <int> <int>
#> 1 Bacteroides genus 631 282
#> 2 Prevotella genus 624 318
#> 3 Lachnospiraceae family 594 264
#> 4 Streptococcus genus 579 363
#> 5 Lactobacillus genus 521 317
#> 6 Oscillospiraceae family 456 225
#> 7 Bacillota phylum 452 212
#> 8 Bifidobacterium genus 434 225
#> 9 Faecalibacterium genus 434 155
#> 10 Veillonella genus 392 239
#> 11 Blautia genus 378 171
#> 12 Pseudomonadota phylum 377 243
#> 13 Actinomycetota phylum 376 202
#> 14 Clostridium genus 366 176
#> 15 Ruminococcus genus 338 136
#> 16 Roseburia genus 336 107
#> 17 Eubacteriales order 330 147
#> 18 Bacteroidota phylum 329 152
#> 19 Haemophilus genus 325 128
#> 20 Enterobacteriaceae family 317 218
#> # ℹ 11 more variables: decreased_signatures <int>, `Binomial Test pval` <dbl>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <chr>, species <chr>, n_signatures <int>, metaphlan_name <fct>