apply_qvalue {edge} | R Documentation

## Estimate the q-values for a given set of p-values

### 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)

[Package edge version 2.12.2 Index]