relevel_function: Relevel and rung DESEQ2 analysis
In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

relevel_function

R Documentation

Relevel and rung DESEQ2 analysis

Description

When running DESeq2 you sometimes require to relevel some comparisons

Usage

relevel_function(
  dds_object,
  category,
  reference,
  given_dir,
  dfAnnotation,
  list_of_cols,
  data_type = "mRNA",
  gene.annot.df.given = NULL,
  int_threads = 2,
  sign_value.given = 0.05,
  LFC.given = log2(1.2),
  comp_ID.given = "comp1",
  forceResults = FALSE,
  localFit = FALSE,
  shrinkage.given = "apeglm"
)

Arguments

`dds_object`	DESeq2 object
`category`	Name of the variable to use within dds_object metadata
`reference`	Name of the reference class to set.
`given_dir`	Output dir to use
`dfAnnotation`	Dataframe containing additional information for each sample
`int_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),
`forceResults`	Boolean to force re-run analysis if already generated in the folder provided
`localFit`	Use a fitType=local for mean dispersion fit in DESeq2
`shrinkage.given`	LFC shrinkage estimator provided. Available: apeglm, ashr or normal