findMarkers: Find marker genes for each cluster

In iCellR: Analyzing High-Throughput Single Cell Sequencing Data

Description

This function takes an object of class iCellR and performs differential expression (DE) analysis to find marker genes for each cluster.

Usage

findMarkers(
  x = NULL,
  data.type = "main",
  pval.test = "t.test",
  p.adjust.method = "hochberg",
  fold.change = 2,
  padjval = 0.1,
  Inf.FCs = FALSE,
  uniq = FALSE,
  positive = TRUE
)

Arguments

x	An object of class iCellR.
data.type	Choose from "main", "atac", "atac.imputed" 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".
fold.change	A number that designates the minimum fold change for out put, default = 2.
padjval	Minimum adjusted p value for out put, default = 0.1.
Inf.FCs	If set to FALSE the infinite fold changes would be filtered from out put, default = FALSE.
uniq	If set to TRUE only genes that are a marker for only one cluster would be in the out put, default = FALSE.
positive	If set to FALSE both the up regulated (positive) and down regulated (negative) markers would be in the out put, default = TRUE.

Value

An object of class iCellR

iCellR documentation built on Oct. 9, 2021, 5:07 p.m.