diffEndTest {tradeSeq}R Documentation

Perform statistical test to check for DE between final stages of every lineage.

Description

Assess differential expression between the end points of lineages of a trajectory.

Usage

diffEndTest(models, ...)

## S4 method for signature 'SingleCellExperiment'
diffEndTest(models, global = TRUE,
  pairwise = FALSE, l2fc = 0)

## S4 method for signature 'list'
diffEndTest(models, global = TRUE, pairwise = FALSE,
  l2fc = 0)

Arguments

models

Typically the output from fitGAM, either a list of fitted GAM models, or an object of SingleCellExperiment class.

...

parameters including:

global

If TRUE, test for all pairwise comparisons simultaneously.

pairwise

If TRUE, test for all pairwise comparisons independently.

l2fc

Numeric: log2 fold change threshold to test against. Note, that this only applies to the pairwise comparisons, the global test will be unaffected.

Details

The l2fc argument allows to test against a particular fold change threshold. For example, if the interest lies in discovering genes that are differentially expressed with an absolute log2 fold change cut off above 1, i.e. a fold change of at least 2, then one can test for this by setting l2fc=1 as argument to the function.

Value

A matrix with the wald statistic, the number of df and the p-value associated with each gene for all the tests performed. If the testing procedure was unsuccessful, the procedure will return NA test statistics and p-values.

Examples

data(gamList, package = "tradeSeq")
diffEndTest(gamList, global = TRUE, pairwise = TRUE)

[Package tradeSeq version 1.0.1 Index]