PERFect is a novel permutation filtering approach designed to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds, and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. Methods are assessed on two `mock' experiment data sets, where the true taxa compositions are known, and are applied to a publicly available vaginal microbiome data set. The method correctly removes contaminant taxa in `mock' data sets, quantifies and visualizes the corresponding filtering loss, and provides a uniform data-driven filtering criteria for real microbiome data sets.
|Author||Ekaterina Smirnova [aut, cre] Quy Cao [cre]|
|Maintainer||Quy Cao <[email protected]>|
|License||GPL (>= 3)|
|Package repository||View on GitHub|
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