findMarkers: Find marker genes for each cluster

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Find marker genes for each cluster

Description

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

Usage

findMarkers(x = NULL, fold.change = 2, padjval = 0.1, Inf.FCs = F,
  uniq = F, positive = TRUE)

Arguments

x	An object of class scSeqR.
fold.change	A number that designates the minimum fold change for out put, defult = 2.
padjval	Minimum adjusted p value for out put, defult = 0.1.
Inf.FCs	If set to FALSE the infinate fold changes would be filtered from out put, defult = FALSE.
uniq	If set to TRUE only genes that are a marker for only one cluster would be in the out put, defult = TRUE.
positive	If set to FALSE both the up regulated (positive) and down regulated (negetive) markers would be in the out put, defult = FALSE.

Value

An object of class scSeqR

Examples

## Not run: 
marker.genes <- find.markers(my.obj,fold.change = 2,padjval = 0.1,uniq = T)

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.