retrieveTopClustersMarkers,scRNAseq-method {conclus} | R Documentation

## retrieveTopClustersMarkers

### Description

This function retrieves the top N marker genes for each cluster.

### Usage

    retrieveTopClustersMarkers(theObject, nTop=10, removeDuplicates = TRUE,
                    writeMarkerGenes = FALSE)

### Arguments

`theObject` | An Object of class scRNASeq for which rankGenes was run. See ?rankGenes.
`nTop` | Number of marker genes to retrieve per cluster. Default=10.
`removeDuplicates` | If TRUE, duplicated markers are removed from the lists. Default=TRUE.
`writeMarkerGenes` | If TRUE, writes one list per cluster in the output folder defined in theObject, and in the sub-directory marker_genes/markers_lists. Default=FALSE.

### Value

Output the list of markers to marker_genes/markers_lists if writeMarkersGenes is TRUE and return a scRNASeq object with its clustersMarkers slot updated.

### Author(s)

Ilyess RACHEDI, based on code by Polina PAVLOVICH and Nicolas DESCOSTES.

### See Also

retrieveGenesInfo

### Examples

    ## Object scr containing the results of previous steps
    load(system.file("extdata/scrFull.Rdat", package="conclus"))

    ## Retrieve the top 10 markers per cluster
    scr <- retrieveTopClustersMarkers(scr)

[Package conclus version 1.2.4 Index]