findMarkers: Find marker genes for each cluster

Description Usage Arguments Value Examples

Description

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

Usage

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findMarkers(
  x = NULL,
  data.type = "main",
  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" and "imputed", default = "main"

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 = FALSE.

Value

An object of class iCellR

Examples

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marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = FALSE)

head(marker.genes)

iCellR documentation built on Nov. 16, 2020, 9:13 a.m.

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