trajectoryDE: Differential trajectory testing.

In nlhuong/vistimeseq: Analysis for short time-series data

Description

Performs differential trajectory testing for timecourse data using adonis method.

Usage

trajectoryDE(
  object,
  dist_method = "euclidean",
  p_adj_method = "BH",
  lambda = c(0.5, 0.25),
  verbose = TRUE,
  ...
)

Arguments

object	A TimeSeriesExperiment object.
dist_method	the name of any method used in vegdist to calculate pairwise distances, "euclidean" by defaults.
p_adj_method	a correction method. See details in p.adjust. Default is "BH".
lambda	Weights for each lag difference, for time-course data. Length of lambda specifies number of lags to include. Default is c(0.5, 0.25) for lag 1 and 2. Used only if 'timecourse.data' slot not initialized.
verbose	whether code comments should be printed. Default is TRUE.
...	other options to adonis function from vegan.

Value

a data.frame with adonis results for all features.

Examples

data("endoderm_small")
endoderm_small <- makeTimeSeries(endoderm_small)
## Not run: 
   endoderm_small <- trajectoryDE(endoderm_small)
   head(differentialExpression(endoderm_small, "trajectory_de"))

## End(Not run)

nlhuong/vistimeseq documentation built on Sept. 4, 2021, 2:41 a.m.