associationTest: Perform statistical test to check whether gene expression is...

In tradeSeq: trajectory-based differential expression analysis for sequencing data

Description

This test assesses whether average gene expression is associated with pseudotime.

Usage

associationTest(models, ...)

## S4 method for signature 'SingleCellExperiment'
associationTest(models, global = TRUE, lineages = FALSE, l2fc = 0)

## S4 method for signature 'list'
associationTest(models, global = TRUE, lineages = FALSE, l2fc = 0)

Arguments

models	The fitted GAMs, typically the output from fitGAM.
...	parameters including:
global	If TRUE, test for all lineages simultaneously.
lineages	If TRUE, test for all lineages independently.
l2fc	The log2 fold change threshold to test against. Note, that this will affect both the global test and the pairwise comparisons.

Value

A matrix with the wald statistic, the number of degrees of freedom and the p-value associated with each gene for all the tests performed. If the testing procedure was unsuccessful, the procedure will return NA.

Examples

set.seed(8)
data(crv, package="tradeSeq")
data(countMatrix, package="tradeSeq")
sce <- fitGAM(counts = as.matrix(countMatrix),
                  sds = crv,
                  nknots = 5)
assocRes <- associationTest(sce)

tradeSeq documentation built on Nov. 8, 2020, 7:51 p.m.