likelihood_rank: Likelihood ranks

In strayMat/lineageDE: Differentially expressed genes in cell lineages

Description

compute vgam ranks with likelihood ratio test p-values and aic difference criteria

Usage

likelihood_rank(data, reg.f = "loess", pval = F, span = 0.75, s.df = 4,
  fam = "gaussian", dtw = F)

Arguments

data	a warpDEDataSet with results to be plotted.
reg.f	the regression method to use, either "loess" with the gam package, "ns" which fits a natural cubic spline with gam package or "splines" which fits a smoothing spline (default is "loess").
pval	logical, if the pval criteria is to be computedor not (default is F).
span	numeric, a smoothing parameter for the regression function (default is 0.75, see gam::lo for details).
s.df	numeric, a smoothing parameter for the nsplines regregression (default is 4, see splines::s for details about regularization).
fam	character, for the vgam regression, the distribution assumption of the residuals; etiher "binomial" or "gaussian" (default is "gaussian").
dtw	logical, if the alignment should be made with dtw before acomputing the likelihood, (default is FALSE) .

Value

returns rankingDE objects: one for the likelihood ratio test pvalues and one for the aic difference criteria if aic == T.

strayMat/lineageDE documentation built on May 30, 2019, 8:18 a.m.