model_bayes: Model differential expression

In latlio/tidyde: Tidy Differential Expression

Description

'model_bayes()' performs an empirical Bayes fit

Usage

model_bayes(.fit, .f = limma::eBayes, ...)

Arguments

.fit	an MArrayLM object produced by 'model_limma()' or 'make_contrasts()'
.f	limma::eBayes
...	additional arguments to .f

Details

Please refer to eBayes for more information.

Value

a 'list' ('MArrayLM') object containing the results of the fit

Examples

counts <- readr::read_delim("data/GSE60450_Lactation-GenewiseCounts.txt", delim = "\t")
meta <- readr::read_delim("data/SampleInfo_Corrected.txt", delim = "\t") %>%
  mutate(FileName = stringr::str_replace(FileName, "\\.", "-"))

id <- as.character(counts$EntrezGeneID)
check_sample_names(counts, c(1,2), meta, FileName) %>%
  purrr::pluck("mod_count") %>%
  filter_genes(., id, "edgeR") %>%
  make_voom(., my_design) %>%
  model_limma() %>%
  make_contrasts(Statuspregnant, Statusvirgin) %>%
  model_bayes()

latlio/tidyde documentation built on Dec. 21, 2021, 9:40 a.m.