individual: Individuals sampled in experiment

In jdstorey/edge: Extraction of Differential Gene Expression

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)

jdstorey/edge documentation built on May 18, 2019, 11:35 p.m.