run_glmm_nb_design: Differential Expression with Negative Binomial Mixed Models

In amcdavid/GeneseeBulk: Pipeline, analysis functions and markdown templates for bulk RNAseq

Differential Expression with Negative Binomial Mixed Models

Description

Differential Expression with Negative Binomial Mixed Models

Usage

run_glmm_nb_design(
  dge_,
  formula_,
  assay_ = "counts",
  subset_,
  method = c("nebula", "glmer.nb"),
  ...
)

Arguments

dge_	DESeq2::DESeqDataSet() object
formula_	formula() with a simple random intercept
assay_	which assay in dge_ to use
subset_	an R expression, as a character, evaluated in the context of colData(dge_) to subset the columns (samples)
method	character
...	passed to lme4::glmer.nb() or nebula::nebula()

Value

an object with a tidy, results and resultNames method

amcdavid/GeneseeBulk documentation built on March 26, 2022, 4:58 a.m.