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 2025-01-30 21:57:36
createTaxonTable(full.dat, n=20)
#> # A tibble: 20 × 15
#> `Taxon Name` `Taxonomic Level` total_signatures increased_signatures
#> <chr> <chr> <int> <int>
#> 1 Prevotella genus 520 276
#> 2 Streptococcus genus 481 299
#> 3 Bacteroides genus 458 198
#> 4 Lactobacillus genus 428 259
#> 5 Lachnospiraceae family 399 155
#> 6 Bacillota phylum 366 169
#> 7 Bifidobacterium genus 364 179
#> 8 Faecalibacterium genus 346 119
#> 9 Veillonella genus 312 195
#> 10 Oscillospiraceae family 304 137
#> 11 Pseudomonadota phylum 299 184
#> 12 Actinomycetota phylum 291 159
#> 13 Clostridium genus 279 143
#> 14 Blautia genus 277 115
#> 15 Fusobacterium genus 266 157
#> 16 Bacteroidota phylum 264 128
#> 17 Haemophilus genus 257 98
#> 18 Ruminococcus genus 245 94
#> 19 Enterobacteriaceae family 245 170
#> 20 Eubacteriales order 244 107
#> # 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>