core {microbiome} | R Documentation |
Filter the phyloseq object to include only prevalent taxa.
core(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. |
... |
Arguments to pass. |
Filtered phyloseq object including only prevalent taxa
Contact: Leo Lahti microbiome-admin@googlegroups.com
Salonen A, Salojarvi J, Lahti L, de Vos WM. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16-20, 2012 To cite the microbiome R package, see citation('microbiome')
core_members, variable_members, noncore_members
data(dietswap) # Detection threshold 0 (strictly greater by default); # Prevalence threshold 50 percent (strictly greater by default) pseq <- core(dietswap, 0, 50/100)