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]