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]