retrieveTopClustersMarkers-scRNAseq: retrieveTopClustersMarkers

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

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)

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.