omega: Omega calcularion

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

View source: R/omega.R

Description

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

Usage

1
omega(XA, XB, na, nb, m, alpha = 0.05, distr = "norm")

Arguments

XA

a numeric vector values of condition A

XB

a numeric vector values of condition b

na

a numeric value, sample size in A.

nb

a numeric value, sample size in B

m

simulation number specified.

alpha

a numeric value, statistical cutoff. Default is 0.05.

distr

data distribution specified for data. For current version, we consider three distributions: normal, negative binomial (NB) and uniform. Default distribution is "norm". If user believe that the data follow negative binomial distribution, then set distr="NB" or "negative binomial" or if the data follow uniform distribution, then set distr="unif"or "uniform".

Details

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

Value

return a numeric value

Author(s)

Yuan-De Tan [email protected]

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

momega, rhov

Examples

1
2
3
4
5
6
7
8
X<-c(112,122,108,127)
Y<-c(302, 314,322,328)
omega(XA=X, XB=Y, na=4, nb=4, m=2000, alpha = 0.05)
#[1] 0.9055152
 omega(XA=X, XB=Y, na=4, nb=4, m=2000, alpha = 0.05,distr="NB")
#[1] 0.8995424
omega(XA=X, XB=Y, na=4, nb=4, m=2000, alpha = 0.05,distr="uniform")
#[1] 0.97194

Yuande/tatest documentation built on May 7, 2019, 10:55 a.m.