betattest: Beta t-test

In NBBttest: Negative Binomial Beta t-Test

Beta t-test

Description

Beta t-test and degree of freedom for each gene or isoform are calculated in this function.

Usage

betattest(X, na, nb, NX=100, level)

Arguments

X	count data of RNA sequence reads containing N genes (or isoforms).
na	number of replicate libraries in condition A.
nb	number of replicate libraries in condition B.
NX	numeric value. It is used at level="isoform". NX=100 is default but does not used at any level.
level	string, has three options: "isoform" or "sgRNA"

Details

In beta t-test,

t=\frac{(P_A-P_B)}{√(V_A+V_B)}

where P_A and P_B are proportions of a gene or an isoform in conditions A and B, V_A and V_B are variances of this gene or isoform in conditions A and B, respectively. They are output of betaparametVP.

Value

return two lists:

t	t-value list.
df	df list. df is degree of freedom.

Note

In our method, pooled standard error > 0 in any case, so the t-statistics alway has definition.

Author(s)

Yuan-De Tan [e-mail]

References

Baggerly KA, Deng L, Morris JS, Aldaz CM (2003) Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics, 19: 1477-1483.
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. 2015 DOI: 10.1371/journal.pone.0123658.

See Also

pratio, oddratio.

Examples

data(jkttcell) 
X<-jkttcell[1:100,]
na<-3
nb<-3
cn<-ncol(X)
rn<-nrow(X)
XC<-X[,1:(cn-na-nb)]
XX<-X[,(cn-na-nb+1):cn]
betattest<-betattest(X=XX, na=3,nb=3, level="isoform")

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