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

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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.