LikelihoodRatioTest {grandR}

Compute a likelihood ratio test.

Description

The test is computed on any of total/old/new counts using DESeq2 based on two nested models specified using formulas.

Usage

LikelihoodRatioTest(
  data,
  name = "LRT",
  mode = "total",
  slot = "count",
  normalization = mode,
  target = ~Condition,
  background = ~1,
  columns = NULL,
  logFC = FALSE,
  verbose = FALSE
)

Arguments

data

A grandR object

name

the user defined analysis name to store the results

mode

either "total", "new" or "old"

slot

which slot to use (should be a count slot, not normalized values)

normalization

normalize on "total", "new", or "old" (see details)

target

formula specifying the target model (you can use any column name from the Coldata(data))

background

formula specifying the background model (you can use any column name from the Coldata(data))

columns

logical vector of which columns (samples or cells) to use (or NULL: use all)

logFC

compute and add the log2 fold change as well

verbose

Print status updates

Details

This is a convenience wrapper around the likelihood ratio test implemented in DESeq2.

DESeq2 by default performs size factor normalization. When computing differential expression of new RNA, it might be sensible to normalize w.r.t. to total RNA, i.e. use the size factors computed from total RNA instead of computed from new RNA. This can be accomplished by setting mode to "new", and normalization to "total"!

Value

a new grandR object including a new analysis table. The columns of the new analysis table are

"M"

the base mean

"S"

the difference in deviance between the reduced model and the full model

"P"

the likelihood ratio test P value

"Q"

same as P but Benjamini-Hochberg multiple testing corrected

"LFC"

the log2 fold change for the target model (only with the logFC parameter set to TRUE)