betattest: Beta t-test

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/betattest.R

Description

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

Usage

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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

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 estimated in conditions A and B. They are outputted by betaparametVP.

Value

return two lists:

t

t-value list.

df

df list. df is degree of freedom.

Note

If pooled standard error is zero, then the t-value is not defined and set to be zero.

Author(s)

Yuan-De Tan [email protected]

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

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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)

Yuande/MBttest documentation built on April 29, 2018, 8:05 a.m.