startVsEndTest {tradeSeq} | R Documentation |
Assess differential expression between the start and end points of a lineage.
startVsEndTest(models, ...) ## S4 method for signature 'SingleCellExperiment' startVsEndTest(models, global = TRUE, lineages = FALSE, pseudotimeValues = NULL) ## S4 method for signature 'list' startVsEndTest(models, global = TRUE, lineages = FALSE, pseudotimeValues = NULL)
models |
the list of GAMs, typically the output from
|
... |
parameters including: |
global |
If TRUE, test for all lineages simultaneously. |
lineages |
If TRUE, test for all lineages independently. |
pseudotimeValues |
a vector of length 2, specifying two pseudotime values to be compared against each other, for every lineage of the trajectory. @details Note that this test assumes that all lineages start at a pseudotime value of zero, which is the starting point against which the end point is compared. |
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. If both global
and lineages
are TRUE, then a matrix
of p-values is returned.
data(gamList, package = "tradeSeq") startVsEndTest(gamList, global = TRUE, lineages = TRUE)