spgs (version 1.0-1)

chargaff2.test: Matrix Test of CSPR for Dinucleotides

Description

Performs the matrix test of Chargaff's second parity rule (CSPR) for dinucleotides proposed in Hart and Mart<ed>nez (2011).

Usage

chargaff2.test(x, alg=c("table", "simulate", "upper"), n, no.p.value=FALSE)

Arguments

x

either a vector containing the relative frequencies of each of the 4 nucleotides A, C, G, T, a character vector representing a DNA sequence in which each element contains a single nucleotide, or a DNA sequence stored using the SeqFastadna class from the seqinr package.

alg

the algorithm for computing the p-value. If set to “simulate”, the p-value is obtained via Monte Carlo simulation. If set to “upper”, an analytic upper bound on the p-value is computed. “upper” are based on formulae in Hart and Mart<ed>nez (2011). If type is specified as “table” (the default value),the p-value for the test is obtained from a linear interpolation of a look-up table. See the note below for further details.

n

The number of replications to use for Monte Carlo simulation. If computationally feasible, a value >= 10000000 is recommended.

no.p.value

If TRUE, do not compute the p-value. The default is FALSE.

Value

A list with class "htest.ext" containing the following components:

statistic

the value of the test statistic.

p.value

the p-value of the test. Only included if no.p.value is FALSE.

method

a character string indicating what type of test was performed.

data.name

a character string giving the name of the data.

f

the 5-element vector used in calculating the test statistic.

estimate

the stochastic matrix \(\hat P\) used to derive the test statistic.

stat.desc

a brief description of the test statistic.

null

the null hypothesis (\(H_0\)) of the test.

alternative

the alternative hypothesis (\(H_1\)) of the test.

Details

This function performs a test of Chargaff's second parity rule for dinucleotides based on a 4X4 stochastic matrix \(\hat P\) estimated from the empirical dinucleotide distribution of a genomic sequence . The \(a,b)\) entry of \(\hat P\) gives the empirical probability (relative frequency) that a nucleotide \(a\) is followed by a nucleotide \(b\) in the sequence. The test is set up as follows:

\(H_0\): the sequence (or matrix \(\hat P\)) does not comply with CSPR for dinucleotides \(H_1\): the sequence (or matrix \(\hat P\)) complies with CSPR for dinucleotides

References

Hart, A.G. and Mart<ed>nez, S. (2011) Statistical testing of Chargaff's second parity rule in bacterial genome sequences. Stoch. Models 27(2), 1--46.

See Also

chargaff0.test, chargaff1.test agct.test, ag.test, chargaff.gibbs.test

Examples

# NOT RUN {
#Demonstration on real bacterial sequence
data(nanoarchaeum)
chargaff2.test(nanoarchaeum)

#Simulate synthetic DNA sequence that does not satisfy Chargaff's second parity rule
trans.mat <- matrix(c(.4, .1, .4, .1, .2, .1, .6, .1, .4, .1, .3, .2, .1, .2, .4, .3), 
ncol=4, byrow=TRUE)
seq <- simulateMarkovChain(500000, trans.mat, states=c("a", "c", "g", "t"))
chargaff2.test(seq)
# }