deseq_lrt: Bring together some of the likelihood ratio test analyses.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Bring together some of the likelihood ratio test analyses.

Description

This function hopes to wrap up some of the ideas/methods for LRT.

Usage

deseq_lrt(
  expt,
  interactor_column = "visitnumber",
  interest_column = "clinicaloutcome",
  transform = "rlog",
  factors = NULL,
  cutoff = 0.05,
  minc = 3,
  interaction = TRUE
)

Arguments

expt	Input expressionset
interactor_column	Potentially interacting metadata
interest_column	Essentially the condition in other analyses.
transform	DESeq2 transformation applied (vst or rlog).
factors	Other factors of interest
cutoff	Significance cutoff
minc	Minimum number of elements for a group
interaction	Use an interaction model?

See Also

DOI:10.1186/s13059-014-0550-8

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.