apply_sva {edge} | R Documentation |
Runs sva
on the null and full models in
deSet
. See sva
for additional details.
apply_sva(object, ...) ## S4 method for signature 'deSet' apply_sva(object, ...)
object |
|
... |
Additional arguments for |
deSet
object where the surrogate variables
estimated by sva
are added to the full model and null model
matrices.
John Storey, Jeffrey Leek, Andrew Bass
Leek JT, Storey JD (2007) Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis. PLoS Genet 3(9): e161. doi:10.1371/journal.pgen.0030161
Leek JT and Storey JD. (2008) A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences, 105: 18718- 18723.
# 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 surrogate variable analysis de_sva <- apply_sva(de_obj) # run odp/lrt with surrogate variables added de_odp <- odp(de_sva, bs.its = 30) summary(de_odp)