apply_qvalue {edge} | R Documentation |
Runs qvalue
on a deSet
object.
apply_qvalue(object, ...) ## S4 method for signature 'deSet' apply_qvalue(object, ...)
object |
|
... |
Additional arguments for |
deSet
object with slots updated by qvalue
calculations.
John Storey, Andrew Bass
Storey JD and Tibshirani R. (2003) Statistical significance for genome-wide studies. Proceedings of the National Academy of Sciences, 100: 9440-9445
# import data library(splines) 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 lrt (or odp) and apply_qvalue de_lrt <- lrt(de_obj) de_lrt <- apply_qvalue(de_lrt, fdr.level = 0.05, pi0.method = "bootstrap", adj=1.2) summary(de_lrt)