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

In edge: Extraction of Differential Gene Expression

Description

Runs qvalue on a deSet object.

Usage

apply_qvalue(object, ...)

## S4 method for signature 'deSet'
apply_qvalue(object, ...)

Arguments

object	S4 object: deSet
...	Additional arguments for qvalue

Value

deSet object with slots updated by qvalue calculations.

Author(s)

John Storey, Andrew Bass

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)

edge documentation built on Nov. 8, 2020, 6:48 p.m.