run.diff.exp: Differential expression (DE) analysis

run.diff.expR Documentation

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


iCellR documentation built on May 29, 2024, 5:14 a.m.

Related to run.diff.exp in iCellR...