Ibb Manual
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Package ‘ibb’
Title The (inverted) beta-binomial test for count data
Version 12.12.12
Date 2012-12-12
Author Thang V. Pham
Maintainer Thang V. Pham <t.pham@vumc.nl>
Description 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).
License All rights reserved by the author. This software package is provided for research purposes in a
non-commercial environment. Please do not redistribute.
Rtopics documented:
bb.test ................................................. 1
ibb.test................................................. 2
Index 4
bb.test 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
xA vector or matrix of counts. When xis 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.
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Author(s)
Thang V. Pham <t.pham@vumc.nl>
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
# example proteomics spectral count data
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)
######################
# comparing 3 groups: columns c(1, 2, 3), c(4, 5, 6), and c(7, 8) of a data file
d <- read.delim("example-3groups.txt", header = TRUE)
# compare 3 groups, using all available CPU cores
out <- bb.test(d[, 1:8], colSums(d[, 1:8]), c(rep("a", 3), rep("b", 3), rep("c", 2)),
n.threads = 0)
# write result to file
write.table(cbind(d, out$p.value), file = "example-3groups-out.txt",
sep = "\t", row.names = FALSE)
ibb.test The inverted beta-binomial test
Description
Performs the inverted beta-binomial test for paired count data.
Usage
ibb.test(x, tx, group, alternative = c("two.sided", "less", "greater"), n.threads = 1)
Arguments
xA vector or matrix of counts. When xis a matrix, the test is performed row by row.
tx A vector or matrix of the total sample counts. When tx is a matrix, the number of rows
must be equal to the number of rows of x.
group A vector of group indicators. There should be two groups of equal size. The samples are
matched by the order of appearance in each group.
alternative A character string specifying the alternative hypothesis: "two.sided" (default), "greater"
or "less".
n.threads The number of threads to be used.
2
Details
This test is designed for paired count data, for example data acquired before and after treatment.
Value
A list of values is returned:
p.value The p-value of the test.
fc An estimation of the common fold change.
Author(s)
Thang V. Pham <t.pham@vumc.nl>
References
Pham TV, Jimenez CR (2012) An accurate paired sample test for count data. Bioinformatics, 28(18):i596-i602.
Examples
# example RNA-seq read count data
x <- c(33, 32, 86, 51, 52, 149)
tx <- c(7742608, 15581382, 20933491, 7126839, 13842297, 14760103)
group <- c(rep("cancer", 3), rep("normal", 3))
ibb.test(x, tx, group)
######################
# columns c(1, 2, 3) are respectively paired with columns c(4, 5, 6)
d <- read.delim("example-paired.txt", header = TRUE)
# perform a paired test for all rows, using all but one CPU cores
out <- ibb.test(d[, 1:6], colSums(d[, 1:6]), c(rep("pre", 3), rep("post", 3)),
n.threads = -1)
# write result to file
write.table(cbind(d, out$fc, out$p.value), file = "example-paired-out.txt",
sep = "\t", row.names = FALSE)
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