View source: R/seurat_wrapper.R
object_ref | R Documentation |
Function to convert labelled object to avg expression matrix
object_ref(input, ...) ## Default S3 method: object_ref( input, cluster_col = NULL, var_genes_only = FALSE, assay_name = NULL, method = "mean", lookuptable = NULL, if_log = TRUE, ... ) ## S3 method for class 'Seurat' object_ref( input, cluster_col = NULL, var_genes_only = FALSE, assay_name = NULL, method = "mean", lookuptable = NULL, if_log = TRUE, ... ) ## S3 method for class 'SingleCellExperiment' object_ref( input, cluster_col = NULL, var_genes_only = FALSE, assay_name = NULL, method = "mean", lookuptable = NULL, if_log = TRUE, ... )
input |
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 |
lookuptable |
if not supplied, will look in built-in table for object parsing |
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
object_ref( s_small3, cluster_col = "RNA_snn_res.1" )
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