deSet {edge} | R Documentation |
Creates a deSet
object that extends the
ExpressionSet
object.
deSet(object, full.model, null.model, individual = NULL) ## S4 method for signature 'ExpressionSet' deSet(object, full.model, null.model, individual = NULL)
object |
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full.model |
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null.model |
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individual |
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deSet
object
It is essential that the null and full models have the same variables as the ExpressionSet phenoType column names.
John Storey, Andrew Bass
# import data library(splines) data(kidney) age <- kidney$age sex <- kidney$sex kidexpr <- kidney$kidexpr cov <- data.frame(sex = sex, age = age) pDat <- as(cov, "AnnotatedDataFrame") exp_set <- ExpressionSet(assayData = kidexpr, phenoData = pDat) # create models null_model <- ~sex full_model <- ~sex + ns(age, df = 4) # create deSet object from data de_obj <- deSet(exp_set, null.model = null_model, full.model = full_model) # optionally add individuals to experiment, in this case there are 36 # individuals that were sampled twice indSamples <- as.factor(rep(1:36, each = 2)) de_obj <- deSet(exp_set, null.model = null_model, full.model = full_model, ind = indSamples) summary(de_obj)