dinucleotideFrequencyTest     package:Biostrings     R Documentation

Pearson's chi-squared Test and G-tests for String Position Dependence

Description:

     Performs Person's chi-squared test, G-test, or William's corrected
     G-test to determine dependence between two nucleotide positions.

Usage:

       dinucleotideFrequencyTest(x, i, j, test = c("chisq", "G", "adjG"),
                                 simulate.p.value = FALSE, B = 2000)

Arguments:

       x: A DNAStringSet or RNAStringSet object. 

    i, j: Single integer values for positions to test for dependence. 

    test: One of '"chisq"' (Person's chi-squared test), '"G"' (G-test),
          or '"adjG"' (William's corrected G-test). See Details
          section. 

simulate.p.value: a logical indicating whether to compute p-values by
          Monte Carlo simulation. 

       B: an integer specifying the number of replicates used in the
          Monte Carlo test. 

Details:

     The null and alternative hypotheses for this function are:

     H0:  positions 'i' and 'j' are independent

     H1:  otherwise

     Let O and E be the observed and expected probabilities for base
     pair combinations at positions 'i' and 'j' respectively. Then the
     test statistics are calculated as:

     'test="chisq"':  stat = sum(abs(O - E)^2/E)

     'test="G"':  stat = 2 * sum(O * log(O/E))

     'test="adjG"':  stat = 2 * sum(O * log(O/E))/q, where q = 1 + ((df
          - 1)^2 - 1)/(6*length(x)*(df - 2))

     Under the null hypothesis, these test statistics are approximately
     distributed chi-squared(df = ((distinct bases at i) - 1) *
     ((distinct bases at j) - 1)).

Value:

     An htest object. See help(chisq.test) for more details.

Author(s):

     P. Aboyoun

References:

     Ellrott, K., Yang, C., Sladek, F.M., Jiang, T. (2002) "Identifying
     transcription factor binding sites through Markov chain
     optimations", Bioinformatics, 18 (Suppl. 2), S100-S109.

     Sokal, R.R., Rohlf, F.J. (2003) "Biometry: The Principle and
     Practice of Statistics in Biological Research", W.H. Freeman and
     Company, New York.

     Tomovic, A., Oakeley, E. (2007) "Position dependencies in
     transcription factor binding sites", Bioinformatics, 23, 933-941.

     Williams, D.A. (1976) "Improved Likelihood ratio tests for
     complete contingency tables", Biometrika, 63, 33-37.

See Also:

     'nucleotideFrequencyAt', XStringSet-class, 'chisq.test'

Examples:

       data(HNF4alpha)
       dinucleotideFrequencyTest(HNF4alpha, 1, 2)
       dinucleotideFrequencyTest(HNF4alpha, 1, 2, test = "G")
       dinucleotideFrequencyTest(HNF4alpha, 1, 2, test = "adjG")

