preseqR

Code in this repository aims to expand the functionality of Preseq and make it available in the R statistical computing enviroment. There are five ways this is supposed to work:

1. The basic functionality of the preseq program, initially focusing only on library complexity, is available. These functions contain the string “rfa” as part of their names.

2. The mathematical routines for doing rational function approximation via continued fractions were implemented as a wrapper for existing functionality in C++. This changed since version 3.1.1, and now all functionality is in R.

3. Fitting a zero-truncated negative binomial distribution to the sample is available. These functions include the string “ztnb” as part of the names.

4. The simulation module is used to generate samples based on mixture of Poisson.

5. Extra functions are provided to estimate the number of species represented at least r times in a random sample.

See the preseqR package on CRAN for details

UPDATE HISTORY

Updates in version 4.0.0

1. Improve the user interface for core functions
2. Add functions to optimize the depth of single-cell whole-genome sequencing experiments and whole-exome sequencing experiments
3. Add functions to predict the sample coverage, which is the probability of sampling an observed species from a population
4. Add functions to predict the fraction of k-mers represented at least r times in a sequencing experiment

Updates in version 3.1.2

1. Fixed a bug for removing defects

Updates in version 3.1.1

1. Substituted embedded C++ code with R code
2. Removed the dependencies on the software preseq

Updates in version 3.0.1

1. Fixed a bug in Chao’s estimator
2. Fixed issues for a Solaris C++ compiler.

Updates in version 3.0.0

1. We have changed the return types of many functions in the package. These functions no longer generate estimated accumulative curves. Instead, they return function types, which are estimators for the number of species represented by at least r indivdiduals in a random sample.
2. We added several estimators for predicting the number of species represented by at least r individuals in a random sample

Updates in version 2.1.1

We have changed the interfaces for most of our exported functions. We add new estimators for the number of species represented by at least r individuals in a random sample.

INSTALLATION

1. We recommand everyone to install the package preseqR from CRAN. It can be easily done by in an R session by typing:

   >install.packages("preseqR")

2. The following instructions are for installing the package from the source. Assume the source code of preseqR has been pulled from the git repo and it is under the current directory. Start a session in an R interpreter and type:

   >install.packages("polynom")
   >install.packages("preseqR", repos=NULL, type="source")

   Note that the package polynom is required by preseqR.

CONTACTS AND BUG REPORTS

Andrew D. Smith andrewds@usc.edu

COPYRIGHT AND LICENSE INFORMATION

Copyright (C) 2017-2022 Chao Deng and Andrew D. Smith

Authors: Chao Deng and Andrew D. Smith

This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.