diffEndTest {tradeSeq} | R Documentation |
Assess differential expression between the end points of lineages of a trajectory.
diffEndTest(models, ...) ## S4 method for signature 'SingleCellExperiment' diffEndTest(models, global = TRUE, pairwise = FALSE, l2fc = 0) ## S4 method for signature 'list' diffEndTest(models, global = TRUE, pairwise = FALSE, l2fc = 0)
models |
Typically the output from
|
... |
parameters including: |
global |
If TRUE, test for all pairwise comparisons simultaneously. |
pairwise |
If TRUE, test for all pairwise comparisons independently. |
l2fc |
Numeric: log2 fold change threshold to test against. Note, that this only applies to the pairwise comparisons, the global test will be unaffected. |
The l2fc
argument allows to test against a particular fold change
threshold. For example, if the interest lies in discovering genes that are
differentially expressed with an absolute log2 fold change cut off above 1,
i.e. a fold change of at least 2, then one can test for this by setting
l2fc=1
as argument to the function.
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.
data(gamList, package = "tradeSeq") diffEndTest(gamList, global = TRUE, pairwise = TRUE)