Creates differential expression results — plot_wrapper_DE

The function will create a folder called DE_results_(conditonal or temporal), it will then create a summary heatmap of all the differential expression experiments done in that type.

The function will then iterate over the differential gene expression experiments done in either DE_type (conditional or temporal) and creates two csv files, one containing the raw differential expression data and the other is a subset of the raw data containing only the significant genes The function also creates a volcano plot and MA plot for each experiment

The individual differential expression results are stored in folders which carry the name of the experiment

plot_wrapper_DE_results(
  object,
  DE_type,
  genes_of_interest = c(),
  results_folder = "TS_results/",
  adjust_missing_temp_samples = TRUE,
  do_SVGs = TRUE,
  do_heatmap = TRUE
)

Arguments

object: A timeseries object
DE_type: The type of differential gene expression done that the function will use to create results. Either conditional or temporal
genes_of_interest: A vector of genes of interest, can be empty (c())
results_folder: The main folder where the results will be stored
adjust_missing_temp_samples: Boolean indicating if missing temporal samples should be compensated for (NA introduced). Currently, there is no reason to have this set to False.
do_SVGs: Boolean indicating if SVGs should be saved for the heatmaps
do_heatmap: Boolean indicating if the custom heatmap should be performed

Value

None