Description Usage Arguments Value Examples
Calculate cells and genes distances, rank them per cell and extract top n features
1 2 3 4 5 6 7 8 9 | GetCellGeneSet(X, reduction = "mca", dims, features, cells, n.features)
## S3 method for class 'Seurat'
GetCellGeneSet(X, reduction = "mca", dims = seq(50),
features = NULL, cells = NULL, n.features = 200)
## S3 method for class 'SingleCellExperiment'
GetCellGeneSet(X, reduction = "MCA",
dims = seq(50), features = NULL, cells = NULL, n.features = 200)
|
X |
Seurat or SingleCell Experiment Object |
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 |
Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loadings |
cells |
Character vector of cell names to subset cell coordinates. If not specified will take all features available from specified reduction Embeddigns. |
n.features |
single integer specifying how many top features should be extracted from the ranking |
A cell named list of gene rankings ordererd by distances from shortest (most specfic) to farthest (less specific)
1 2 | seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5)
GroupGeneRanking <- GetGroupGeneRanking(seuratPbmc, group.by = "seurat_clusters", dims = 1:5)
|
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