switchde {switchde} | R Documentation |
Fit sigmoidal differential expression models to gene expression across pseudotime. Parameter estimates are returned along with a p-value for switch-like differential expression over a null model (constant expression).
switchde(object, pseudotime = NULL, zero_inflated = FALSE, lower_threshold = 0.01, maxiter = 1000, log_lik_tol = 0.01, verbose = FALSE, sce_assay = "exprs")
object |
Gene expression data that is either
|
pseudotime |
A pseudotime vector with a pseudotime corresponding to
every cell. Can be |
zero_inflated |
Logical. Should zero inflation be implemented? Default |
lower_threshold |
The minimum threshold below which to set expression to zero to avoid numerical issues. Default is 0.01 |
maxiter |
Maximum number of iterations for EM algorithm if zero inflation enabled. Default 100 |
log_lik_tol |
If the change in the log-likelihood falls below this for zero inflated EM the algorithm is assumed to have converged |
verbose |
Print convergence update for EM algorithm |
sce_assay |
The assay from the |
A matrix where each column corresponds to a gene, the first row is the p-value for that gene and subsequent rows are model parameters.
data(synth_gex) data(ex_pseudotime) sde <- switchde(synth_gex, ex_pseudotime)