noncore_members {microbiome} | R Documentation |
Filter the phyloseq object to include only taxa that do not belong to the core set defined by the detection and prevalence thresholds.
noncore_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. |
Filtered phyloseq object including only rare taxa
Contact: Leo Lahti microbiome-admin@googlegroups.com
To cite the microbiome R package, see citation('microbiome')
data(peerj32) pseq <- noncore_members(peerj32$phyloseq, 200, 20/100)