earlyDETest {tradeSeq} | R Documentation |
Perform test of early differences between lineages
Perform test of early differences between lineages
earlyDETest(models, ...) ## S4 method for signature 'SingleCellExperiment' earlyDETest(models, global = TRUE, pairwise = FALSE, knots = NULL, nPoints = 100) ## S4 method for signature 'list' earlyDETest(models, global = TRUE, pairwise = FALSE, knots = NULL, nPoints = 100)
models |
the list of GAMs, typically the output from
|
... |
parameters including: |
global |
If TRUE, test for all pairwise comparisons simultaneously. |
pairwise |
If TRUE, test for all pairwise comparisons independently. |
knots |
A vector of length 2 specifying the knots before and after the branching of interest. |
nPoints |
the number of points to be compared between lineages. |
To help the user in choosing which knots to use when defining the
branching, the plotGeneCount
function has a models optional
parameter that can be used to visualize where the knots are.
A matrix with the wald statistic, the number of df and the p-value associated with each gene for all the tests performed.
data(gamList, package = "tradeSeq") earlyDETest(gamList, knots = c(1, 2), global = TRUE, pairwise = TRUE)