iCellR (version 1.6.1)

top.markers: Choose top marker genes

Description

This function takes the marker genes info if chooses marker gene names for plots.

Usage

top.markers(
  x = NULL,
  topde = 10,
  min.base.mean = 0.2,
  filt.ambig = TRUE,
  cluster = 0
)

Arguments

x

An object of class iCellR.

topde

Number of top differentially expressed genes to be choosen from each cluster, default = 10.

min.base.mean

Minimum base mean of the genes to be chosen, default = 0.5.

filt.ambig

Filter markers that are seen for more than one cluster, default = TRUE.

cluster

Choose a cluster to find markers for. If 0, it would find markers for all clusters, , default = 0.

Value

A set of gene names

Examples

# NOT RUN {
marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE)
top.markers(marker.genes, topde = 10, min.base.mean = 0.8)
# }