run.diff.exp {iCellR}

Differential expression (DE) analysis

Description

This function takes an object of class iCellR and performs differential expression (DE) analysis for clusters and conditions.

Usage

run.diff.exp(
  x = NULL,
  data.type = "main",
  pval.test = "t.test",
  p.adjust.method = "hochberg",
  de.by = "clusters",
  cond.1 = "array",
  cond.2 = "array",
  base.cond = 0
)

Arguments

x

An object of class iCellR.

data.type

Choose from "main" and "imputed", default = "main"

pval.test

Choose from "t.test", "wilcox.test", default = "t.test".

p.adjust.method

Correction method. Choose from "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none", default = "hochberg".

de.by

Choose from "clusters", "conditions", "clustBase.condComp" or "condBase.clustComp".

cond.1

First condition to do DE analysis on.

cond.2

Second condition to do DE analysis on.

base.cond

A base condition or cluster if de.by is either cond.clust or clust.cond

Value

An object of class iCellR