calculateQC: Calculate QC Metrics for Taxa and Samples

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Calculate QC Metrics for Taxa and Samples

Description

Calculate QC Metrics for Taxa and Samples

Usage

calculateQC(x)

Arguments

x	A phyloseq object

Details

Calculate QC metrics for taxa and samples.

Value

A list with two tibbles.

SampleQC

• sample_total_taxa:Total taxa in a sample

• sample_total_reads:Total reads in a sample

• number_taxa_account_fifty_percent:Number of taxa account for 50 percent

TaxaQC

• taxa_counts:Total counts of taxa in all samples

• taxa_mean_counts:Mean counts of taxa in all samples

• taxa_dectected_samples:Number of samples in which taxa detected

• taxa_prevalence:Percent of samples in which taxa detected

Author(s)

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
qc_Data <- calculateQC(FuentesIliGutData)
qc_Data

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.