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]). The required prevalence is strictly greater by default. To include the limit, set include.lowest to TRUE. |
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, rare_members
data(dietswap) # Detection threshold 0 (strictly greater by default); # Prevalence threshold 50 percent (strictly greater by default) pseq <- core(dietswap, 0, 50/100) # Detection threshold 0 (strictly greater by default); # Prevalence threshold exactly 100 percent; for this set # include.lowest=TRUE, otherwise the required prevalence is # strictly greater than 100 pseq <- core(dietswap, 0, 100/100, include.lowest = TRUE)