DESeq2_HCGB_function: DESEq2 main function
In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

DESeq2_HCGB_function

R Documentation

DESEq2 main function

Description

This functions creates the main analysis given a DDS and comparison to test

Usage

DESeq2_HCGB_function(
  dds_object,
  coef_n,
  comp_name,
  comp_ID = "comp1",
  numerator = "example1",
  denominator = "example2",
  OUTPUT_Data_dir,
  df_treatment_Ind,
  list_of_cols,
  threads = 2,
  sign_value.given = 0.05,
  LFC.given = log2(1.2),
  min_cutoff_to_plot = 3,
  max_cutoff_to_plot = 50,
  gene.annot.df = NULL,
  data_type = "mRNA",
  forceResults = FALSE,
  shrinkage = "apeglm"
)

Arguments

`dds_object`	DESeq2 object
`coef_n`	Coefficient number obtain using resultsName(dds)
`comp_name`	Name of the comparison
`comp_ID`	ID tag of the comparison
`numerator`	Name of the numerator comparison
`denominator`	Name of the denominator comparison
`OUTPUT_Data_dir`	Folder path to store results
`df_treatment_Ind`	Dataframe containing additional information for each sample
`list_of_cols`	Set of columns with important information in df_treatment_ind
`threads`	Number of CPUs to use (Default: 2).
`sign_value.given`	Adjusted pvlaue cutoff. Default=0.05,
`LFC.given`	Log Fold change cutoff. Default=log2(1.2),
`min_cutoff_to_plot`	Minimun number of genes significant to continue analysis. Default=3
`max_cutoff_to_plot`	Number of genes significant to plot as candidates analysis. Default=50
`gene.annot.df`	Dataframe containing gene annotation (Default: NULL)
`forceResults`	Boolean to force re-run analysis if already generated in the folder provided