iCellR (version 1.5.1)

findMarkers: 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",
  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

# NOT RUN {
marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = FALSE)

head(marker.genes)
# }