earlyDETest {tradeSeq} | R Documentation

## Perform test of early differences between lineages

### Description

Perform test of early differences between lineages

Perform test of early differences between lineages

### Usage

    earlyDETest(models, ...)

    ## S4 method for signature 'SingleCellExperiment'
    earlyDETest(models, global = TRUE,
      pairwise = FALSE, knots = NULL, nPoints = 100)

    ## S4 method for signature 'list'
    earlyDETest(models, global = TRUE, pairwise = FALSE,
      knots = NULL, nPoints = 100)

### Arguments

`models` | the list of GAMs, typically the output from `fitGAM`.
`...` | parameters including:
`global` | If TRUE, test for all pairwise comparisons simultaneously.
`pairwise` | If TRUE, test for all pairwise comparisons independently.
`knots` | A vector of length 2 specifying the knots before and after the branching of interest.
`nPoints` | the number of points to be compared between lineages.

### Details

To help the user in choosing which knots to use when defining the branching, the `plotGeneCount` function has a models optional parameter that can be used to visualize where the knots are.

### Value

A matrix with the wald statistic, the number of df and the p-value associated with each gene for all the tests performed.

### Examples

    data(gamList, package = "tradeSeq")
    earlyDETest(gamList, knots = c(1, 2), global = TRUE, pairwise = TRUE)

[Package tradeSeq version 1.0.1 Index]