assessTrajectoryTrends: Trajectory trend analysis

In kueckelj/SPATA: A Toolbox for Spatial Gene Expression Analysis

Trajectory trend analysis

Description

Analyzes the trend of gene and gene-set-expressions along trajectories by fitting a variety of mathematical models to them and by assessing the quality of the fit.

• assessTrajectoryTrends(): Takes a valid spata-object and constructs the subsequent data.frame from scratch.

• assessTrajectoryTrends2(): Takes a summarized trajectory data.frame returned by getTrajectoryDf().

Usage

assessTrajectoryTrends(
  object,
  trajectory_name,
  of_sample = "",
  variables,
  accuracy = 5,
  verbose = TRUE
)

assessTrajectoryTrends2(stdf, verbose = TRUE)

Arguments

object	A valid spata-object.
trajectory_name	The trajectory of interest specified as a single character value.
of_sample	The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
variables	Character vector. The variables of interest: Gene sets: Must be in getGeneSets() Genes: Must be in getGenes() Features: Must be numeric ones of getFeatureNames()
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
stdf	A summarized trajectory data.frame. (e.g. obtained by getTrajectoryDf()).

Value

A data.frame arranged by the residuals area-under-the-curve-values describing how well a model fitted the expression trend of a gene or gene set.

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.