coreOTU {PathoStat} | R Documentation |
Compute Core OTUs for the given data matrix
coreOTU(zcounts, otuthreshold = 0.05, prevalence = 0.4)
zcounts |
Standardized counts |
otuthreshold |
Abundance cutoff threshold for the OTU to be picked |
prevalence |
Prevalence of the OTU at threshold cutoff among samples |
list containing core OTUs
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)