patternTest {tradeSeq}R Documentation

Assess differential expression pattern between lineages.

Description

Assess differences in expression patterns between lineages.

Usage

patternTest(models, ...)

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

## S4 method for signature 'SingleCellExperiment'
patternTest(models, global = TRUE,
  pairwise = FALSE, 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.

nPoints

the number of points to be compared between lineages.

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")
patternTest(gamList, global = TRUE, pairwise = TRUE)

[Package tradeSeq version 1.0.1 Index]