get_diff_model: Get Differential TSS/TSR models

In zentnerlab/TSRexploreR: TSS and TSR Analysis

Get Differential TSS/TSR models

Description

Get the DESeq2 or edgeR model.

Usage

get_diff_model(experiment, data_type = c("tss", "tsr"))

Arguments

experiment	TSRexploreR object.
data_type	Either 'tss' or 'tsr'.

Value

DESeq2 or edgeR differential expression model.

Examples

data(TSSs)
sample_sheet <- data.frame(
  sample_name=c(
    sprintf("S288C_D_%s", seq_len(3)),
    sprintf("S288C_WT_%s", seq_len(3))
  ),
  file_1=rep(NA, 6), file_2=rep(NA, 6),
  condition=c(
    rep("Diamide", 3),
    rep("Untreated", 3)
  )
)

exp <- TSSs %>%
  tsr_explorer(sample_sheet=sample_sheet) %>%
  format_counts(data_type="tss") %>%
  fit_de_model(~condition, data_type="tss", method="edgeR")

dm <- get_diff_model(exp, data_type="tss")

zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.