compute_sim_voomlike: Computing simulations results

In tcgsaseq: Time-Course Gene Set Analysis for RNA-Seq Data

Description

Computing simulations results

Usage

compute_sim_voomlike(
  counts,
  design,
  gs_keep,
  indiv,
  alternative = FALSE,
  fixed_eff = 0.5,
  fixed_eff_sd = 0,
  rand_eff_sd = 0.25,
  RE_indiv_sd = NULL,
  eps_sd = 0.05,
  alpha_DEseq = 0.05
)

Examples

## Not run: 
data_sims <- data_sim_voomlike(seed=1)
res <- compute_sim_voomlike(counts = data_sims$counts,
                           design = data_sims$design,
                           gs_keep = data_sims$gs_keep,
                           indiv = data_sims$indiv,
                           alternative=TRUE,
                           fixed_eff = 0.5,
                           fixed_eff_sd = 0,
                           rand_eff_sd = 0,
                           RE_indiv_sd=NULL)
res_all <- cbind(res$res_voom, res$res_perso, res$res_noweights, res$res_DEseq, res$res_edgeR)
colnames(res_all) <- c(paste0(rep(c("asym", "perm", "camera", "roast"), 3),
                             rep(c("_voom", "_perso", "_noweights"), each=4)),
                      paste0("DESeq2_minTest_", c("exact", "approx", "CN")), "roast_edgeR")

## End(Not run)

tcgsaseq documentation built on Sept. 13, 2020, 5:13 p.m.