DESeq2_test: differential expression analysis of RNASeq data using DESeq2

Usage

DESeq2_test(
  data,
  column,
  groups,
  reference = "WT",
  covariates = c(),
  speedup = FALSE,
  parallel = FALSE
)

data: data matrix of counts data
column: column name of the groups to be used for the definitions
groups: design matrix containing the definitions to be compared.
reference: Reference group to use in the DE analysis
covariates: List of column names in the design matrix to be used as covariates
speedup: Boolean parameter to indicate if the faster version of DESeq2 should be used with fitType = "glmGamPoi" (note: it may not work depending on the system)
parallel: Boolean parameter to indicate if DESeq2 should be run in parallel mode

DESeq2 result object with the pvalues, adjusted pvalues and foldchanges of the DE analysis

# Internal function