Identfies taxa above certain abundance and prevalence thresholds, that can be quantitatively analyzed
measurable_taxa(...) # S3 method for default measurable_taxa(Tab, min_reads_otu = 25, min_samples_otu = 5, method = "absolute", table = TRUE) # S3 method for Dataset measurable_taxa(Dat, min_reads_otu = 25, min_samples_otu = 5, method = "absolute", table = TRUE, clean = TRUE)
| Tab | Count table matrix. Samples as columns and OTUs as rows. |
|---|---|
| method | Either "absolute" (min absolute number of reads in min number of sample) or "AbsProp" (absolute number if reads and proportion of samples). |
| table | logical indicating whether an abundance table should be returned |
| Dat | A |
| clean | logical, indicating whether the function |
When table = FALSE, it returns a logical index vector that shows which taxa pass the thresholds.
When table = TRUE, it returns a matrix or Dataset object (depending on the method used), where samples that do not pass the thresholds have been removed
Implments abundance filters defined in Benson et al.(2010) & Lundberg et al. (2012). It is recommended to threshold any Dataset before any quantitative analysis.
1. Benson AK, Kelly S a, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18933–8. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2973891&tool=pmcentrez&rendertype=abstract
2. Lundberg DS, Lebeis SL, Herrera Paredes S, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. Nature Publishing Group; 2012 Aug 1;488(7409):86–90. Available from: http://www.nature.com/doifinder/10.1038/nature11237