betaApproxNBTest {edgeR}R Documentation

An Approximate Exact Test for Differences between Two Negative Binomial Groups

Description

Approximate the tail probabilities of a conditional negative binomial exact test of equality of means between groups.

Usage

betaApproxNBTest(x1, x2, dispersion)

Arguments

x1

vector of observed negative binomial variables for group one

x2

vector of observed negative binomial variables for group two

dispersion

vector or scalar providing the value of the NB dispersion parameter for each tag to be used for calculating p-values for differences in mean between the two groups.

Details

exactTest is the user-level function for computing p-values for differential expression between groups in DGE data. However, for tags with extremely large counts, the computation of the tail propbabilities of the conditional negative binomial exact test can be unstable. For such tags, the tail probabilities are well approximated by using a transformed beta distribution (Anderson and Boullion, 1972).

Value

Vector of p-values providing the extent of evidence for difference in means between the two groups.

Author(s)

Davis McCarthy

References

Anderson, Dwane E. and Boullion, Thomas L. Homogeneity test for two negative binomial populations. IEEE Transactions on Reliability, Vol. R-21, No. 2, May 1972.

See Also

Computing p-values for differential expression for each transcript between two (only) digital gene expression libraries can also be done using the sage.test function in the statmod package.

Examples

# generate raw counts from NB, create list object
x1<-rnbinom(20,size=1,mu=1000)
x2<-rnbinom(20, size=1, mu=1500)
betaApproxNBTest(x1, x2, dispersion=1)

[Package edgeR version 2.4.3 Index]