seurat_ref {clustifyr} | R Documentation |
Function to convert labelled seurat object to avg expression matrix
seurat_ref(seurat_object, ...) ## S3 method for class 'Seurat' seurat_ref( seurat_object, cluster_col = "classified", var_genes_only = FALSE, assay_name = NULL, method = "mean", subclusterpower = 0, if_log = TRUE, ... )
seurat_object |
seurat_object after tsne or umap projections and clustering |
... |
additional arguments |
cluster_col |
column name where classified cluster names are stored in seurat meta data, cannot be "rn" |
var_genes_only |
whether to keep only var_genes in the final matrix output, could also look up genes used for PCA |
assay_name |
any additional assay data, such as ADT, to include. If more than 1, pass a vector of names |
method |
whether to take mean (default) or median |
subclusterpower |
whether to get multiple averages per original cluster |
if_log |
input data is natural log, averaging will be done on unlogged data |
reference expression matrix, with genes as row names, and cell types as column names
ref <- seurat_ref(s_small3, cluster_col = "RNA_snn_res.1")