findMarkers: Find marker genes for each cluster

In iCellR: Analyzing High-Throughput Single Cell Sequencing Data

Find marker genes for each cluster

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,
  low.cell.filt = 5,
  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.
low.cell.filt	filter out clusters with low number of cells, default = 5.
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 May 29, 2024, 5:14 a.m.