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]