NBBttest (version 1.0.1)

betattest: 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"

Value

return two lists:

t

t-value list.

df

df list. df is degree of freedom.

Details

In beta t-test, $$t=\frac{(P_A-P_B)}{\sqrt(V_A+V_B)}$$ 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.

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

# NOT RUN {
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")
# }