edge (version 2.4.2)

apply_qvalue: Estimate the q-values for a given set of p-values

Description

Runs qvalue on a deSet object.

Usage

apply_qvalue(object, ...)
## S3 method for class 'deSet':
apply_qvalue(object, ...)

Arguments

object

S4 object: deSet

...

Additional arguments for qvalue

Value

• deSet object with slots updated by qvalue calculations.

References

Storey JD and Tibshirani R. (2003) Statistical significance for genome-wide studies. Proceedings of the National Academy of Sciences, 100: 9440-9445

See Also

deSet, odp and lrt

Examples

# import data
library(splines)
data(kidney)
age <- kidney$age
sex <- kidney$sex
kidexpr <- kidney$kidexpr
cov <- data.frame(sex = sex, age = age)

# create models
null_model <- ~sex
full_model <- ~sex + ns(age, df = 4)

# create deSet object from data
de_obj <- build_models(data = kidexpr, cov = cov, null.model = null_model,
full.model = full_model)

# Run lrt (or odp) and apply_qvalue
de_lrt <- lrt(de_obj)
de_lrt <- apply_qvalue(de_lrt, fdr.level = 0.05,
pi0.method = "bootstrap", adj=1.2)
summary(de_lrt)