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

In rezakj/iCellR: Analyzing High-Throughput Single Cell Sequencing Data

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

rezakj/iCellR documentation built on March 29, 2024, 6:55 p.m.