variable_members {microbiome} | R Documentation |
Filter the phyloseq object to include only variable taxa.
variable_members(x, detection, prevalence, include.lowest = FALSE)
x |
|
detection |
Detection threshold for absence/presence (strictly greater by default). |
prevalence |
Prevalence threshold (in [0, 1]; strictly greater by default) |
include.lowest |
Include the lower boundary of the detection and prevalence cutoffs. FALSE by default. |
Variable taxa are members of the microbiota that are not rare, and not members of the core microbiota. Such taxa reach notable abundance in a notable fraction of the population. The variable members are calculated by using the indicated prevalence threshold to define rare taxa; and its complement 1-prevalence to define core taxa. The remaining taxa are considered variable. The same detection threshold is used in all cases.
Filtered phyloseq object including only variable taxa.
Contact: Leo Lahti microbiome-admin@googlegroups.com
To cite the microbiome R package, see citation('microbiome')
core_members, core, rare
data(dietswap) # Detection threshold 0 (strictly greater by default); # Prevalence threshold 50 percent (strictly greater by default) pseq.rel <- transform(dietswap, 'compositional') pseq <- variable_members(pseq.rel, 0.5/100, 20/100)