Get the most frequently occurring taxa in a table of signatures

Get the most frequently occurring taxa in a table of signatures

getMostFrequentTaxa(
  dat,
  n = 10,
  sig.type = c("both", "increased", "decreased"),
  direction.column = "Abundance in Group 1"
)

Arguments

dat

A table such as output by importBugSigDB

n

Number of most frequently occurring taxa to return

sig.type

increased for increased in cases relative to controls, decreased for decreased in cases relative to controls, both for either

direction.column

column containing direction information in dat

Value

A list of signatures, with PMIDs for list element names

Examples

full.dat <- bugsigdbr::importBugSigDB()
#> Using cached version from 2022-03-31 12:35:22
getMostFrequentTaxa(full.dat)
#> 
#>                 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus 
#>                                                                                                          221 
#>                 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella 
#>                                                                                                          191 
#>                k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 
#>                                                                                                          179 
#>                 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus 
#>                                                                                                          171 
#>                                                                                    k__Bacteria|p__Firmicutes 
#>                                                                                                          155 
#>                                                                                 k__Bacteria|p__Bacteroidetes 
#>                                                                                                          152 
#>                                  k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae 
#>                                                                                                          144 
#> k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium 
#>                                                                                                          138 
#>             k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium 
#>                                                                                                          121 
#>               k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella 
#>                                                                                                          121