qvalueObj {edge} | R Documentation

## Access/set qvalue slot

### Description

These generic functions access and set the `qvalue` object in the `deSet` object.

### Usage

    qvalueObj(object)

    qvalueObj(object) <- value

    ## S4 method for signature 'deSet'
    qvalueObj(object)

    ## S4 replacement method for signature 'deSet'
    qvalueObj(object) <- value

### Arguments

`object` | `S4 object`: `deSet`
`value` | S3 `object`: `qvalue`

### Value

`qvalueObj` returns a `qvalue` object.

### Author(s)

John Storey, Andrew Bass

### See Also

`lrt`, `odp` and `deSet`

### Examples

    # import data
    library(splines)
    library(qvalue)
    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 the odp method
    de_odp <- odp(de_obj, bs.its = 20)

    # extract out significance results
    qval_obj <- qvalueObj(de_odp)

    # run qvalue and assign it to deSet slot
    pvals <- qval_obj$pvalues
    qval_new <- qvalue(pvals, pfdr = TRUE, fdr.level = 0.1)
    qvalueObj(de_odp) <- qval_new

[Package edge version 2.24.0 Index]