individual {edge} | R Documentation

## Individuals sampled in experiment

### Description

These generic functions access and set the individual slot in `deSet`.

### Usage

    individual(object)

    individual(object) <- value

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

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

### Arguments

`object` | `deSet`
`value` | `factor`: Identifies which samples correspond to which individuals. Important if the same individuals are sampled multiple times in a longitudinal fashion.

### Value

`individual` returns information regarding dinstinct individuals sampled in the experiment.

### Author(s)

John Storey, Andrew Bass

### See Also

`deSet`

### Examples

    library(splines)
    # import data
    data(endotoxin)
    ind <- endotoxin$ind
    time <- endotoxin$time
    class <- endotoxin$class
    endoexpr <- endotoxin$endoexpr
    cov <- data.frame(individual = ind, time = time, class = class)

    # create ExpressionSet object
    pDat <- as(cov, "AnnotatedDataFrame")
    exp_set <- ExpressionSet(assayData = endoexpr, phenoData = pDat)

    # formulate null and full models in experiement
    # note: interaction term is a way of taking into account group effects
    mNull <- ~ns(time, df=4, intercept = FALSE)
    mFull <- ~ns(time, df=4, intercept = FALSE) +
    ns(time, df=4, intercept = FALSE):class + class

    # create deSet object
    de_obj <- deSet(exp_set, full.model = mFull, null.model = mNull,
    individual = ind)

    # extract out the individuals factor
    ind_exp <- individual(de_obj)

[Package edge version 2.18.0 Index]