GetGroupGeneRanking {CelliD} | R Documentation |
Gene Specificity Ranking Calculation
GetGroupGeneRanking(X, group.by, reduction, dims, features) ## S3 method for class 'Seurat' GetGroupGeneRanking( X, group.by = NULL, reduction = "mca", dims = seq(50), features = NULL ) ## S3 method for class 'SingleCellExperiment' GetGroupGeneRanking( X, group.by, reduction = "MCA", dims = seq(50), features = NULL )
X |
Seurat or SingleCellExperiment object, alternatively a matrix. |
group.by |
column name of meta.data (Seurat) or ColData (SingleCellExperiment) |
reduction |
Which dimensionality reduction to use, must be based on MCA. |
dims |
A vector of integers indicating which dimensions to use with reduction embeddings and loadings for distance calculation. |
features |
A character vector of features name to subset feature coordinates for distance calculation. |
List of genes ranking for each groups
seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5) GroupGeneRanking <- GetGroupGeneRanking(seuratPbmc, group.by = "seurat_clusters", dims = 1:5)