associationTest {tradeSeq} | R Documentation |
This test assesses whether average gene expression is associated with pseudotime.
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)
models |
The fitted GAMs, typically the output from
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... |
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. |
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.
set.seed(8) data(crv, package="tradeSeq") data(countMatrix, package="tradeSeq") sce <- fitGAM(counts = as.matrix(countMatrix), sds = crv, nknots = 5) assocRes <- associationTest(sce)