getClusterGene: Identifying cluster specific genes under clutering from...
In Fang0828/SCMarker: What the package does (short line)

Description Usage Arguments Value Examples

Identifying cluster specific genes under clutering from Seurat or dbscan

1	getClusterGene(obj, method)

`obj`	The list objective from the function SCcluster
`method`	clutering results from "Seurat" or "dbscan"

\res

clustergeneA data frame including cluster specfic genes

data(melanoma)
melanoma1=as.matrix(melanoma[,2:dim(melanoma)[2]])
row.names(melanoma1)=melanoma[,1]
res=ModalFilter(data=melanoma1,geneK=10,cellK=10)
res=GeneFilter(obj=res)
res=getMarker(obj=res,MNN=200,MNNIndex=20)
res=SCcluster(obj=res)
res=getClusterGene(obj=res,method="Seurat")

## The function is currently defined as
function (obj, method) 
{
    marker = obj$marker
    if (method == "Seurat") {
        seuratCluster = obj$seuratCluster
        gene = get_marker_genes(obj$rawdata[marker, names(seuratCluster)], 
            seuratCluster)
        gene$gene = marker
        obj$clustergene = gene
        obj$method = method
    }
    else if (method == "dbscan") {
        dbscanCluster = obj$dbscanCluster
        gene = get_marker_genes(obj$rawdata[marker, names(dbscanCluster)], 
            dbscanCluster)
        gene$gene = marker
        obj$clustergene = gene
        obj$method = method
    }
    return(obj)
  }