startVsEndTest {tradeSeq} | R Documentation

## Perform statistical test to check for DE between starting point and the end stages of every lineage

### Description

Assess differential expression between the start and end points of a lineage.

### Usage

    startVsEndTest(models, ...)

    ## S4 method for signature 'SingleCellExperiment'
    startVsEndTest(models, global = TRUE,
      lineages = FALSE, pseudotimeValues = NULL)

    ## S4 method for signature 'list'
    startVsEndTest(models, global = TRUE,
      lineages = FALSE, pseudotimeValues = NULL)

### Arguments

`models` | the list of GAMs, typically the output from `fitGAM`.
`...` | parameters including:
`global` | If TRUE, test for all lineages simultaneously.
`lineages` | If TRUE, test for all lineages independently.
`pseudotimeValues` | a vector of length 2, specifying two pseudotime values to be compared against each other, for every lineage of the trajectory. @details Note that this test assumes that all lineages start at a pseudotime value of zero, which is the starting point against which the end point is compared.

### 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. If both `global` and `lineages` are TRUE, then a matrix of p-values is returned.

### Examples

    data(gamList, package = "tradeSeq")
    startVsEndTest(gamList, global = TRUE, lineages = TRUE)

[Package tradeSeq version 1.0.1 Index]