patternTest: Assess differential expression pattern between lineages.
In tradeSeq: trajectory-based differential expression analysis for sequencing data

Description Usage Arguments Value Examples

Assess differences in expression patterns between lineages.

patternTest(models, ...)

## S4 method for signature 'list'
patternTest(
  models,
  global = TRUE,
  pairwise = FALSE,
  nPoints = 2 * nknots(models),
  l2fc = 0,
  eigenThresh = 0.01
)

## S4 method for signature 'SingleCellExperiment'
patternTest(
  models,
  global = TRUE,
  pairwise = FALSE,
  nPoints = 2 * nknots(models),
  l2fc = 0,
  eigenThresh = 0.01
)

`models`	The fitted GAMs, typically the output from `fitGAM`.
`...`	parameters including:
`global`	If TRUE, test for all pairwise comparisons simultaneously. If `models` contains conditions (i.e. `fitGAM` was run with the conditions argument), then we compare the within-lineage average across conditions, between lineages.
`pairwise`	If TRUE, return output for all pairwise comparisons made.
`nPoints`	The number of points to be compared between lineages. Defaults to twice the number of knots
`l2fc`	The log2 fold change threshold to test against. Note, that this will affect both the global test and the pairwise comparisons.
`eigenThresh`	Eigenvalue threshold for deciding on the rank of the variance-covariance matrix of the contrasts defined by 'patternTest', and to use for calculating the Wald test statistics. Lower values are more lenient to adding more information but also decrease computational stability. This argument should in general not be changed by the user but is provided for back-compatability. Set to `1e-8` to reproduce results of older version of 'tradeSeq'.

A matrix with the wald statistic, the number of df and the p-value associated with each gene for all the tests performed. Also, for each possible pairwise comparision, the observed log fold changes. If the testing procedure was unsuccessful, the procedure will return NA test statistics, fold changes and p-values.