get_Results_DDS: Generate results given a DDS object
In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

get_Results_DDS

R Documentation

Generate results given a DDS object

Description

When running DESeq2 you usually add multiple terms to the matrix design. Test the effect of them

Usage

get_Results_DDS(
  dds_object,
  OUTPUT_Data_dir_given,
  dfAnnotation,
  list_of_cols,
  comp_ID,
  sign_value.given = 0.05,
  LFC.given = log2(1.2),
  int_threads = 2,
  coef_n = NA,
  forceResults = FALSE,
  min_cutoff_to_plot = 3,
  max_cutoff_to_plot = 50,
  gene.annot = NULL,
  data_type = "mRNA",
  shrinkage.given = "apeglm"
)

Arguments

`dds_object`	DESeq2 object (DESeqDataSet)
`OUTPUT_Data_dir_given`	Absolute path to store results
`dfAnnotation`	Dataframe with useful metadata to include
`comp_ID`	Tag name to include for each comparison
`sign_value.given`	Adjusted pvlaue cutoff. Default=0.05,
`LFC.given`	Log Fold change cutoff. Default=log2(1.2),
`int_threads`	Number of threads to use in the analysis
`coef_n`	Number of the coefficient of results to test (if desired)
`forceResults`	Boolean to force re-run analysis if already generated in the folder provided
`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`	Dataframe containing gene annotation (Default: NULL)
`shrinkage.given`	LFC shrinkage estimator provided. Available: apeglm, ashr or normal