Welcome to project ibb
This R package contains two functions. The beta-binomial test (bb.test) can be used for significance analysis of independent samples (two or more groups). The inverted beta-binomial test (ibb.test) can be used for paired sample testing (e.g. pre-treatment and post-treatment data).
All rights reserved by the author. This software package is provided for research purposes in a non-commercial environment. Please do not redistribute.
The beta-binomial test
Description
Performs the beta-binomial test for count data.
Usage
bb.test(x, tx, group, alternative = c("two.sided", "less", "greater"), n.threads = 1)
Arguments
x: A vector or matrix of counts. When x a matrix, the test is performed row by row.
tx: A vector or matrix of the total sample counts. When tx is a matrix, the number of rows must be equal to the number of rows of x.
group: A vector of group indicators.
alternative: A character string specifying the alternative hypothesis: "two.sided" (default), "greater" or "less".
n.threads: The number of threads to be used.
Details
When n.threads is 0, the maximal number of CPU cores is used. When n.threads is -1, one CPU core less than the maximum is used, and so on.
Value
A list with a single component is returned:
p.value: The p-value of the test.
Author
Thang V. Pham <t.pham@…>
References
Pham TV, Piersma SR, Warmoes M, Jimenez CR (2010) On the beta binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics, 26(3):363-369.
Examples
x <- c(1, 5, 1, 10, 9, 11, 2, 8)
tx <- c(19609, 19053, 19235, 19374, 18868, 19018, 18844, 19271)
group <- c(rep("cancer", 3), rep("normal", 5))
bb.test(x, tx, group)
The inverted beta-binomial test
Description
Performs the inverted beta-binomial test for paired count data.
Usage
ibb.test(x, tx, group, alternative = c("two.sided", "less", "greater"), n.threads = 1)
Arguments
x: A vector or matrix of counts. When x is a matrix, the test is performed row by row.
tx: A vector or matrix of the total sample counts. When tx is a matrix, the number of rows must be equal to the number of rows of x.
group: A vector of group indicators. There should be two groups of equal size. The samples are matched by the order of appearance in each group.
alternative: A character string specifying the alternative hypothesis: "two.sided" (default), "greater" or "less".
n.threads: The number of threads to be used.
Details
This test is designed for paired count data, for example data acquired before and after treatment.
Value
A list of values is returned:
p.value: The p-value of the test.
fc: An estimation of the common fold change.
Author
Thang V. Pham <t.pham@…>
Reference
Pham TV, Jimenez CR (2012) An accurate paired sample test for count data. Bioinformatics, 28(18):i596-i602.
Examples
x <- c(33, 32, 86, 51, 52, 149)
tx <- c(7742608, 15581382, 20933491, 7126839, 13842297, 14760103)
group <- c(rep("cancer", 3), rep("normal", 3))
ibb.test(x, tx, group)
Other NBIC software projects
All active NBIC software projects can be accessed from the project index.
