individual {edge} | R Documentation |
These generic functions access and set the individual slot in
deSet
.
individual(object) individual(object) <- value ## S4 method for signature 'deSet' individual(object) ## S4 replacement method for signature 'deSet' individual(object) <- value
object |
|
value |
|
individual
returns information regarding dinstinct individuals
sampled in the experiment.
John Storey, Andrew Bass
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)