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, nPoints = 2 * tradeSeq::nknots(models), contrastType = "start" ) ## 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. |
nPoints |
The number of points used per lineage to set up the contrast. Defaults to 2 times the number of knots. Note that not all points may end up being actually used in the inference; only linearly independent contrasts will be used. |
contrastType |
The contrast used to impose the log2 fold-change
threshold. Defaults to |
If a log2 fold-change threshold has not been set, we use the QR decompositon
through qr.solve
to invert the variance-covariance matrix of the
contrasts. If instead a log2 fold chalnge-threshold has been set, we invert
that matrix using the Cholesky decomposition through chol2inv
.
A matrix with the wald statistic, the
degrees of freedom and the (unadjusted) p-value
associated with each gene for all the tests performed. If the testing
procedure was unsuccessful for a particular gene, NA
values will be
returned for that gene.
set.seed(8) data(crv, package="tradeSeq") data(countMatrix, package="tradeSeq") sce <- fitGAM(counts = as.matrix(countMatrix), sds = crv, nknots = 5) assocRes <- associationTest(sce)