Description Usage Arguments Value Examples
This test assesses whether average gene expression is associated with pseudotime.
1 2 3 4 5 6 7 | 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
|
... |
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.
1 2 3 4 5 6 7 | set.seed(8)
data(crv, package="tradeSeq")
data(countMatrix, package="tradeSeq")
sce <- fitGAM(counts = as.matrix(countMatrix),
sds = crv,
nknots = 5)
assocRes <- associationTest(sce)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.