preseqR.package: Predicting r-species accumulation curves

In preseqR: Predicting Species Accumulation Curves

Description

The functionality of this package is to predict r-species accumulaiton curves. The method is based on a nonparametric empirical Bayes approach with rational function approximation. The estimator is excellent in accuracy for both large values of r and long-range extrapolations, which are essential to large-scale applications. Some examples are predicting the molecular complexity of sequencing libraries, estimating the minimum sufficient sequencing depths for whole-exome sequencing experiments and optimizing depths for single-cell whole-genome sequencing experiments.

Details

main functions:

preseqR.rSAC

preseqR.rSAC.bootstrap

preseqR.optimal.sequencing

preseqR.rSAC.sequencing.rmdup

preseqR.sample.cov

preseqR.sample.cov.bootstrap

Author(s)

Chao Deng, Timothy Daley, and Andrew D. Smith

Maintainer: Chao Deng <[e-mail]>

References

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Boneh, S., Boneh, A., & Caron, R. J. (1998). Estimating the prediction function and the number of unseen species in sampling with replacement. Journal of the American Statistical Association, 93(441), 372-379.

Chao, A., & Shen, T. J. (2004). Nonparametric prediction in species sampling. Journal of agricultural, biological, and environmental statistics, 9(3), 253-269.

Cohen Jr, A. C. (1960). Estimating the parameters of a modified Poisson distribution. Journal of the American Statistical Association, 55(289), 139-143.

Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature methods, 10(4), 325-327.

Deng C, Daley T & Smith AD (2015). Applications of species accumulation curves in large-scale biological data analysis. Quantitative Biology, 3(3), 135-144. URL http://dx.doi.org/10.1007/s40484-015-0049-7.

Deng, C., Daley, T., Calabrese, P., Ren, J., & Smith, A.D. (2016). Estimating the number of species to attain sufficient representation in a random sample. arXiv preprint arXiv:1607.02804v3.

Efron, B., & Thisted, R. (1976). Estimating the number of unseen species: How many words did Shakespeare know?. Biometrika, 63(3), 435-447.

Efron, B. (1979). Bootstrap methods: another look at the jackknife. The annals of Statistics, 1-26.

Efron, B., & Tibshirani, R. J. (1994). An introduction to the bootstrap. CRC press.

Fisher, R. A., Corbet, A. S., and Williams, C. B. ,1943, The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population, Journal of Animal Ecology, 12, 42-58.

Good, I. J., & Toulmin, G. H. (1956). The number of new species, and the increase in population coverage, when a sample is increased. Biometrika, 43(1-2), 45-63.

Heck Jr, K. L., van Belle, G., & Simberloff, D. (1975). Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology, 1459-1461.

Kalinin V (1965). Functionals related to the poisson distribution and statistical structure of a text. Articles on Mathematical Statistics and the Theory of Probability pp. 202-220.

preseqR documentation built on May 2, 2019, 6:39 a.m.