coreOTUNormalize {PathoStat} | R Documentation |
Compute Empirical Bayes OTU Normalized data
coreOTUNormalize(zcounts, wt = 0.25, otuthreshold = 0.05, prevalence = 0.4)
zcounts |
counts data to be normalized |
wt |
Weight parameter indicating how much information to borrow across samples using Empirical Bayes |
otuthreshold |
Abundance cutoff threshold for the OTU to be picked |
prevalence |
Prevalence of the OTU at threshold cutoff among samples |
list containing Empirical Bayes coreOTU Normalized data
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 coreotunormdat <- coreOTUNormalize(countdat)