Perform statistical test to check for DE between final stages of every lineage.

Assess differential expression between the average expression at the end points of lineages of a trajectory.

diffEndTest(models, ...)

# S4 method for SingleCellExperiment
diffEndTest(models, global = TRUE, pairwise = FALSE, l2fc = 0)

# S4 method for list
diffEndTest(models, global = TRUE, pairwise = FALSE, l2fc = 0)

Arguments

models	The fitted GAMs, typically the output from fitGAM.
...	parameters including:
global	If TRUE, test for all pairwise comparisons simultaneously.
pairwise	If TRUE, test for all pairwise comparisons independently.
l2fc	The log2 fold change threshold to test against. Note, that this will affect both the global test and the pairwise comparisons.

Value

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.

Details

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.

Examples

data(gamList, package = "tradeSeq")
diffEndTest(gamList, global = TRUE, pairwise = TRUE)
#> Only two lineages; skipping pairwise comparison.
#>                   waldStat df    pvalue   logFC1_2
#> 1700012B09Rik 5.952271e-17  1 1.0000000  0.4659914
#> 1700017B05Rik 1.195657e+00  1 0.2741914  2.2271283
#> 1700020L24Rik 5.952271e-17  1 1.0000000  0.4659914
#> 1810009A15Rik 7.361088e-02  1 0.7861501 -0.3283338
#> 1810011H11Rik 5.952271e-17  1 1.0000000  0.4659914
#> 1810027O10Rik 6.182099e-01  1 0.4317133 -0.7828738
#> 1810031K17Rik 8.649102e-01  1 0.3523682  1.0515476
#> 1810033B17Rik 5.952271e-17  1 1.0000000  0.4659914
#> 1810037I17Rik 1.311039e+00  1 0.2522066 -2.6832658
#> 2010002N04Rik 5.952271e-17  1 1.0000000  0.4659914
#> 2010011I20Rik 2.664639e-02  1 0.8703317 21.3959504