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Version 4 (modified by t.pham@…, 6 years ago) (diff)

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Welcome to project ibb



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)


Other NBIC software projects

All active NBIC software projects can be accessed from the project index.