coreOTU {PathoStat}R Documentation

Compute Core OTUs for the given data matrix

Description

Compute Core OTUs for the given data matrix

Usage

coreOTU(zcounts, otuthreshold = 0.05, prevalence = 0.4)

Arguments

zcounts

Standardized counts

otuthreshold

Abundance cutoff threshold for the OTU to be picked

prevalence

Prevalence of the OTU at threshold cutoff among samples

Value

list containing core OTUs

Examples

example_data_dir <- system.file("example/data", package = "PathoStat")
pathoreport_file_suffix <- "-sam-report.tsv"
datlist <- readPathoscopeData(example_data_dir, pathoreport_file_suffix)
countdat <- datlist$countdata
coreotus <- coreOTU(countdat)
[Package PathoStat version 1.4.1 Index]