GetGroupGeneSet {CelliD} | R Documentation |
Extract cluster/group gene sets from MCA
GetGroupGeneSet(X, group.by, reduction, dims, features, n.features) ## S3 method for class 'Seurat' GetGroupGeneSet( X, group.by = NULL, reduction = "mca", dims = seq(50), features = NULL, n.features = 200 ) ## S3 method for class 'SingleCellExperiment' GetGroupGeneSet( X, group.by = NULL, reduction = "MCA", dims = seq(50), features = NULL, n.features = 200 )
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 for distance calculation. |
features |
A character vector of features name to subset feature coordinates for distance calculation. |
n.features |
A single integer specifying how many top features will be extracted from ranking. |
Distance Matrix between groups (column) and genes (row)
seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5) GroupGeneSet <- GetGroupGeneSet(seuratPbmc, dims = 1:5, group.by = "seurat_clusters")