coreOTUNormalize {PathoStat}R Documentation

Compute Empirical Bayes OTU Normalized data

Description

Compute Empirical Bayes OTU Normalized data

Usage

coreOTUNormalize(zcounts, wt = 0.25, otuthreshold = 0.05,
  prevalence = 0.4)

Arguments

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

Value

list containing Empirical Bayes coreOTU Normalized data

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
coreotunormdat <- coreOTUNormalize(countdat)

[Package PathoStat version 1.4.1 Index]