tidiers: Tidying methods for MArrayLM objects

In latlio/tidyde: Tidy Differential Expression

Description

These methods tidy the results of differential expression analysis objects. Currently only 'limma' is supported.

Usage

tidy.marray.lm(x, conf.int = TRUE, exponentiate = FALSE, ...)

Arguments

x	a differential expression fit object. Currently supports 'MArrayLM' from the 'limma' package.
conf.int	logical. Include confidence intervals?
exponentiate	logical. Should the estimates and (if 'conf.int' = 'TRUE') confidence intervals be exponentiated?
...	additional arguments

Value

a 'tbl'

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)
out <- 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()

out %>% tidy.marray.lm()

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