Changes between Version 4 and Version 5 of WikiStart


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Timestamp:
Dec 11, 2012, 1:46:50 PM (7 years ago)
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t.pham@…
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  • WikiStart

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    9 == ''The beta-binomial test'' ==
     9== The beta-binomial test ==
     10[[BR]]
    1011
    1112=== Description ===
     
    5556}}}
    5657
     58[[BR]]
     59
    5760----
     61== The inverted beta-binomial test ==
     62[[BR]]
     63
     64=== Description ===
     65
     66Performs the inverted beta-binomial test for paired count data.
     67
     68=== Usage ===
     69{{{
     70ibb.test(x, tx, group, alternative = c("two.sided", "less", "greater"), n.threads = 1)
     71}}}
     72
     73=== Arguments ===
     74
     75x: A vector or matrix of counts. When x is a matrix, the test is performed row by row.
     76
     77tx: 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.
     78
     79group: 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.
     80
     81alternative: A character string specifying the alternative hypothesis: "two.sided" (default), "greater" or "less".
     82
     83''n.threads'': The number of threads to be used.
     84
     85=== Details ===
     86
     87This test is designed for paired count data, for example data acquired before and after treatment.
     88
     89=== Value ===
     90
     91A list of values is returned:
     92
     93''p.value'': The ''p''-value of the test.
     94
     95''fc'': An estimation of the common fold change.
     96
     97=== Author ===
     98Thang V. Pham <t.pham@vumc.nl>
     99
     100=== Reference ===
     101
     102Pham TV, Jimenez CR (2012) An accurate paired sample test for count data. Bioinformatics, 28(18):i596-i602.
     103
     104=== Examples ===
     105{{{
     106x <- c(33, 32, 86, 51, 52, 149)
     107tx <- c(7742608, 15581382, 20933491, 7126839, 13842297, 14760103)
     108group <- c(rep("cancer", 3), rep("normal", 3))
     109ibb.test(x, tx, group)
     110}}}
     111
     112----
     113
    58114[[BR]]
    59115
    60116== Other NBIC software projects ==
     117
     118[[BR]]
     119
    61120All active NBIC software projects can be accessed from the [https://trac.nbic.nl/ project index].