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This script calculates the conditional uncovered probability for each sample in an OTU table. It uses the methods introduced in Lladser, Gouet, and Reeder, “Extrapolation of Urn Models via Poissonization: Accurate Measurements of the Microbial Unknown” PLoS 2011.
Specifically, it computes a point estimate and a confidence interval using two different methods. Thus it can happen that the PE is actually outside of the CI.
We only provide the ability to generate 95% (alpha=0.95) CIs. The CIs are ULCL CIs; they provide an upper and lower bound, where the lower bound is conservative. The CIs are constructed using an upper-to-lower bound ratio of 10.
The CI method requires precomputed constants that depend on the lookahead. We only provide constants for r=3..25,30,40,50.
Usage: conditional_uncovered_probability.py [options]
The resulting file(s) is a tab-delimited text file, where the columns correspond to estimates of the cond. uncovered probability and the rows correspond to samples. The output file is compatible with the alpha_diversity output files and thus could be tied into the rarefaction workflow.
|PE||Lower Bound||Upper Bound|
To calculate the cond. uncovered probability with the default values, you can use the following command:
conditional_uncovered_probability.py -i otu_table.biom -o cup.txt
To change the accuracy of the prediction change the lookahead value. Larger values of r lead to more precise predictions, but might be unfeasable for small samples. For deeply sequenced samples, try increasing r to 50:
conditional_uncovered_probability.py -i otu_table.biom -o cup_r50.txt -r 50