exactnumci


Exact Numerical Confidence Interval for binomial proportions

Abstract

The package ExactNumCI, available in C++ and R, provides EXACT numerical modeling for inference of Binomial Proportions. In addition it calculates the Confidence Interval (CI) for single binomial proportion, CI for difference of two binomial proportions, and CI for difference of difference. In terms of "EXACT", its result is only restrained by numerical precision tolerance but not by any assumption or approximation.

The method is directly applied in DNA methylation and hydroxymethylation digital analysis, for example in package MOABS.

Comprehensive Document

The PDF version is available at

http://dldcc-web.brc.bcm.edu/lilab/deqiangs/ExactNumCI/ExactNumCI-v1.2.1.pdf

The online HTML version created from 'latex2html' command is available at

http://dldcc-web.brc.bcm.edu/lilab/deqiangs/ExactNumCI/ExactNumCI.html

Download

If you want to use the C++ sources in your project or want to calculate the CI in the Linux terminal, you may download the C++ sources at http://dldcc-web.brc.bcm.edu/lilab/deqiangs/ExactNumCI/ExactNumCI-v1.2.1.tar.gz

We also find it convenient to have the same capability in R terminal. We published the R package ExactNumCI at http://cran.r-project.org/web/packages/ExactNumCI/.

Installation of C++ sources

tar -zxvf ExactNumCI-v1.2.1.tar.gz cd ExactNumCI-v1.2.1 make

Make sure your system has BOOST_ROOT correctly set. For example if your boost include file is in /share/boost-1.46.1/include/, then you need execute the command "export BOOST_ROOT=/share/boost-1.46.1" .

Installation of R package ExactNumCI

You may download the binaries for Windows or Mac. You may also compile the sources R CMD INSTALL ExactNumCI_1.0.0.tar.gz

Since the R package is just a call of C++ sources through the R package Rcpp, you need have Rcpp installed.

Fast Manual

Reference manual for R package is available at http://cran.r-project.org/web/packages/ExactNumCI/. For the detailed the explanation of the methods, please refer to MOABS project.

There are 4 major functions available.

singleCI(k,n) gives the CI for binomial proportion given (k,n).

pdiff(k1,n1,k2,n2, d) gives the probability that the difference of p1 from p2 is greater than d.

pdiffCI(k1,n1, k2,n2) gives the CI for difference of two binomial proportions given (k1,n1, k2, n2).

dodCI(k1,n1, k2,n2, K1, N1,K2,N2) gives the CI for difference of difference (p1-p2) - (P1-P2). At default, a uniform priori distribution of p is assumed. You may also specify the priori distribution parameter a0, b0 by assuming p follows a nonuniform beta distribution beta(a0,b0).

Contact

The C++ package is developed by Deqiang Sun. The R package is developped by Deqiang Sun and Hyun Jung Park.

Please post any questions, suggestions or problems to the exactnumci google group or send email to Deqiang Sun at exactnumci@googlegroups.com.

You are welcome to subscribe to the exactnumci google group for updates.

To cite package ‘ExactNumCI’ in publications use:

Deqiang Sun and Hyun Jung Park (2013). ExactNumCI: Exact Confidence Interval for binomial proportions. R package version 1.0.0. http://CRAN.R-project.org/package=ExactNumCI

A BibTeX entry for LaTeX users is

@Manual{,

title = {ExactNumCI: Exact Confidence Interval for binomial proportions},

author = {Deqiang Sun and Hyun Jung Park},

year = {2013},

note = {R package version 1.0.0},

url = {http://CRAN.R-project.org/package=ExactNumCI},

}

Project Information

The project was created on Feb 1, 2013.

Labels:
Bioinformatics Methylation BinomialProportion ConfidenceInterval Biostatistics Exact