limma_differential: Differential analysis by LIMMA

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Differential analysis by LIMMA

Description

Differential analysis by LIMMA

Usage

limma_differential(
  df,
  group,
  rawcount = FALSE,
  voom = FALSE,
  pre.filter = 0,
  prop.expressed.sample = 0.5,
  cal.AUC = TRUE
)

Arguments

df	raw count or log2(TPM+1), default log2(TPM+1). Must be data.frame, not matrix.
group	factor, first control then experiment
rawcount	true or false
voom	true or false. If library size changed too much.
pre.filter	Cutoff for mean log2(TPM)
prop.expressed.sample	Default 0.5. Proportion of samples have a count greater than pre.filter
cal.AUC	If to calculate AUC

Examples

loonR::limma_differential(tpm.table, group)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.