microbiomeMQC {microbiomeMQC} | R Documentation |
Calculate the 4 key reporting measures for the WHO International Reference Reagents for the microbiome
microbiomeMQC(input, taxonomic_level, output)
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" |
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
No return value. The function writes the results to the specified CSV file.
input <- system.file("extdata", "MQC_testdata.csv", package = "microbiomeMQC")
output <- tempfile(fileext = ".csv")
microbiomeMQC(input, "species", output)