smbetattest: Performance of multiple beta t-test on simulated data

In NBBttest: Negative Binomial Beta t-Test

Performance of multiple beta t-test on simulated data

Description

This function is to peform beta t-test with ρ =1 and ω=1 on simulated data. The result lists differentially expressed genes or isoforms and their ρ values. The ρ values are used to calculate ω value for performance of beta t-tests on the real data.

Usage

smbetattest(X, na, nb, alpha)

Arguments

X	simulated count data with N genes or isoforms.
na	number of replicate libraries in condition A.
nb	number of replicate libraries in condition B.
alpha	statistical probabilistic threshold, default is 0.05.

Details

Before performing NBBttest on real data, user needs ω value for the threshold of ρ. To determine ω value, user is requred to generate a set of null data having the same gene or isoform number and the same numbers of replicate libraries in two conditions and then performs beta t-test on the null datasets by setting ρ =1 and ω =1. In current package, NBBttest can automatically perform the simulation of null data, multiple beta t-test to estimate ω.

Value

Return a set of null ρ values.

Author(s)

Yuan-De Tan [e-mail]

References

Yuan-De Tan Anita M. Chandler, Arindam Chaudhury, and Joel R. Neilson(2015) A Powerful Statistical Approach for Large-scale Differential Transcription Analysis. Plos One. DOI: 10.1371/journal.pone.0123658.

See Also

See Also as mbetattest

Examples

data(skjt) 
nrho<-smbetattest(X=skjt[1:60,],na=3,nb=3,alpha=0.05)

NBBttest documentation built on May 30, 2022, 1:05 a.m.