create_contour: This function fits a 3D regression model for every gene in...

In angy89/TinderMIX: TinderMIX: An R package to cluster gene expression by contour plots

Description

This function fits a 3D regression model for every gene in the dataset and creates an N x N contour plot

Usage

create_contour(exp_data, pheno_data, responsive_genes, dose_index,
  time_point_index, gridSize = 50, pvalFitting.adj.method = "fdr",
  pvalFitting = 0.05, logScale = FALSE, modelSelection = c(1, 2))

Arguments

exp_data	is the expression matrix with genes on the rows and samples on the columns
pheno_data	is a dataframe with phenodata informations. Samples are on the rows. The columns should include the dose and time point information.
responsive_genes	responsive_genes character vector with the genes statistically significant for the two-way anova
dose_index	numeric value specifing the column of the phenodata table containing the doses
time_point_index	numeric value specifing the column of the phenodata table containing the time points
gridSize	numeric value specifing size of the z-grid
logScale	boolean specifying if the fitting is performed by using the dose and time in log or linear scale
modelSelection	is a vector of indices specifying which model to fit. 1:linear 2: poly2, 3: poly3

Value

a list with list with estimated contour objects, 3D fitted objects, fitting statistics and feature values for time and dose

GenesMap	a matrix with the z-maps computed for each gene
RPGenes	a list with the 3D fitted objects
Statis	a matrix witht the fitting statistics: PValue,Adj.R.Square,RMSE
DFList	a list with the data used for the fitting
ModList	a list with the fitted models

angy89/TinderMIX documentation built on Nov. 26, 2020, 9:26 p.m.