rare_members {microbiome} | R Documentation |
Determine members of the rare microbiota with given abundance and prevalence threshold.
rare_members(x, detection = Inf, prevalence = 20/100)
x |
|
detection |
Detection threshold for absence/presence (strictly greater by default). |
prevalence |
Prevalence threshold (in [0, 1]; strictly greater by default) |
For phyloseq object, lists taxa that are less prevalent than the given prevalence threshold. Optionally, never exceeds the given abundance threshold (by default, all abundanecs accepted). For matrix, lists columns that satisfy these criteria.
Vector of rare taxa
Leo Lahti microbiome-admin@googlegroups.com
To cite the microbiome R package, see citation('microbiome')
core_members, noncore_members
data(dietswap) # Detection threshold: the taxa never exceed the given detection threshold # Prevalence threshold 20 percent (strictly greater by default) a <- rare_members(dietswap, detection=100/100, prevalence=20/100)