findMarkers {iCellR} | R Documentation |
This function takes an object of class iCellR and performs differential expression (DE) analysis to find marker genes for each cluster.
findMarkers( x = NULL, data.type = "main", fold.change = 2, padjval = 0.1, Inf.FCs = FALSE, uniq = FALSE, positive = TRUE )
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. |
An object of class iCellR
marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = FALSE) head(marker.genes)