Description Usage Arguments Value
View source: R/create_contour.R
This function fits a 3D regression model for every gene in the dataset and creates an N x N contour plot
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))
|
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 |
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 |
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