check_reduced_LRT: Check the effect of reducing one term from a DESEQ2 design
In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

check_reduced_LRT

R Documentation

Check the effect of reducing one term from a DESEQ2 design

Description

Check reducing effect using LRT method.

Usage

check_reduced_LRT(
  dds_obj.given,
  formula_given,
  comp.folder.given,
  compID.given,
  dfAnnotation.given,
  list_of_cols,
  int_threads = 2,
  sign_value.given = 0.05,
  LFC.given = log2(1.2),
  gene.annot = NULL,
  forceResults = FALSE,
  shrinkage.given = "apeglm"
)

Arguments

`dds_obj.given`	DESeq2 object (DESeqDataSet)
`formula_given`	Formula to substract for formula in dds_obj.given
`comp.folder.given`	Absolute path to store results
`compID.given`	Tag name to include for each comparison
`dfAnnotation.given`	Dataframe with useful metadata to include
`forceResults`	Boolean to force re-run analysis if already generated in the folder provided
`shrinkage.given`	LFC shrinkage estimator provided. Available: apeglm, ashr or normal