warpDE_rank: Wrapper function for all ranking methods

In strayMat/lineageDE: Differentially expressed genes in cell lineages

Description

A wrapper method which takes as input a warpDEDataSet and various options to return the ranking of the genes following one of three methods available: likelihood ratio test, dynamic time warping distance, or dynamic time warping alignment followed by a likelihood ratio test.

Usage

warpDE_rank(data, reg.f = "loess", span = 0.75, splines.df = 4,
  ranking_method = "warpDE")

Arguments

data	a warpDEDataSet with results to be plotted.
reg.f	character, 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").
span	numeric, a smoothing parameter for the regression function if the loess regression (reg.f = 'loess') is used (default is 0.75, see gam::lo for details about regularization).
splines.df	numeric, a smoothing parameter for the nregression function if natural cubic splines (reg.f = 'ns') are used (default is 4, see splines::s for details about regularization).
ranking_method	character, the ranking method to use, either "lrt" for likelihood ratio test, "dtw" for an ordering based solely on dynamic time warping, "warpDE" for a prealable alignment of gene expression with dtw followed by a likelihood ratio test (default is "warpDE").

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.