coreOTUQuantile {PathoStat}R Documentation

Compute coreOTU Quantile Normalized data

Description

Compute coreOTU Quantile Normalized data

Usage

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

Arguments

zcounts

counts data to be normalized

otuthreshold

Abundance cutoff threshold for the OTU to be picked

prevalence

Prevalence of the OTU at threshold cutoff among samples

Value

list containing coreOTU Quantile 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 <- coreOTUQuantile(countdat)

[Package PathoStat version 1.4.1 Index]