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

Description Usage Arguments Value

View source: R/create_contour.R

Description

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

Usage

1
2
3
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.