NBBttest (version 1.0.1)

omega: Omega calcularion

Description

Omega function is a function that is used to estimate omega using simulate null data from negative bionomial distribution. is a null rho that is used as a threshold for real rho. Simulation is dependent on the original data.

Usage

omega(XX, nci, r1, r2, sn, alpha = 0.05)

Arguments

XX

the real dataset.

nci

number of columns for information of data, like gene id, isoform id, gene name, etc.

r1

size of sample 1 or number of replicates in condition 1.

r2

size of sample 2 or number of replicates in condition 2.

sn

number of simulations specified.

alpha

significance level of test. Default value is 0.05.

Value

return a numeric value.

Details

This function is to use null data to calculate omega value with rho = 1.

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. 2015 DOI: 10.1371/journal.pone.0123658.

See Also

pratio and oddratio

Examples

# NOT RUN {
data(jkttcell)	

w<-omega(XX=jkttcell[1:100,],nci=7,r1=3,r2=3,sn=2,alpha=0.05)	
# }