MBttest (version 1.0.0)

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)

Arguments

X

count data of RNA reads containing N genes (or isoforms).

na

number of replicate libraries in condition A

nb

number of replicate libraries in condition B

Value

• return two lists:
• t
  t-value list.
• df
  df list. df is degree of freedom.

Details

In beta t-test, $$t=\frac{(PA-PB)}{sqrt(VA+VB)}$$ where PA and PB are proportions of a gene or an isoform in conditions A and B, VA and VB are variances estimated in conditions A and B. They are outputted by Bag_parametVP.

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[1:1000,]
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(XX,na=3,nb=3)