qvalueObj {edge} | R Documentation |
These generic functions access and set the qvalue
object in the
deSet
object.
qvalueObj(object) qvalueObj(object) <- value ## S4 method for signature 'deSet' qvalueObj(object) ## S4 replacement method for signature 'deSet' qvalueObj(object) <- value
object |
|
value |
S3 |
qvalueObj
returns a qvalue
object.
John Storey, Andrew Bass
# 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