Package 'microbiomeMQC'

Title: Calculate 4 Key Reporting Measures
Description: Perform calculations for the WHO International Reference Reagents for the microbiome. Using strain, species or genera abundance tables generated through analysis of 16S ribosomal RNA sequencing or shotgun sequencing which included a reference reagent. This package will calculate measures of sensitivity, False positive relative abundance, diversity, and similarity based on mean average abundances with respect to the reference reagent.
Authors: Jacob Dehinsilu [aut, cre] , Ravneet Bhuller [aut]
Maintainer: Jacob Dehinsilu <[email protected]>
License: GPL-3
Version: 1.0.2
Built: 2024-12-16 07:01:24 UTC
Source: CRAN

Help Index

Calculate 4 key reporting measures

Description

Calculate the 4 key reporting measures for the WHO International Reference Reagents for the microbiome

Usage

microbiomeMQC(input, taxonomic_level, output)

Arguments

input

Path to the .xlsx or .csv file.e.g. "C:\Users\joeblogs\Desktop\data.xlsx"
taxonomic_level

The taxonomic level ("strain", "species", or "genus") that you are using.
output

Path to save the output CSV file (file path must end with the file name e.g. "C:\Users\joeblogs\Desktop\MQC.csv"

Details

The 4 key reporting measures (using the example of species) are:

Sensitivity: How many species from the reagent are correctly identified.

Diversity: The total number of species detected.

FPRA: The relative abundance of false positives.

Similarity: The Bray-Curtis dissimilarity in composition between the species profile reported and the 'ground truth' profile of the reagent.

To see how the data should be formatted do: data(MQC_testdata) FP = false positive i.e. those bacteria that do not appear in the reagent

Value

No return value. The function writes the results to the specified CSV file.

Examples

input <- system.file("extdata", "MQC_testdata.csv", package = "microbiomeMQC")
output <- tempfile(fileext = ".csv")
microbiomeMQC(input, "species", output)

MQC_testdata

Description

Data used for demonstrating the functionality of the microbiomeMQC package.

Usage

data(MQC_testdata)

Format

An object of class data.frame with 26 rows and 6 columns:

Column1

species

Column2

DNA_hilo_RR

Column3

perfect result

Column4

high FPRA example

Column5

high diversity example

Column6

low sensitivity example

Source

Generated by the package authors for demonstration purposes.