seurat_ref {clustifyr} | R Documentation

## Function to convert labelled seurat object to avg expression matrix

### Description

Function to convert labelled seurat object to avg expression matrix

### Usage

    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,
      ...
    )

    ## 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,
      ...
    )

### Arguments

`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

### Value

reference expression matrix, with genes as row names, and cell types as column names

### Examples

    ref <- seurat_ref(
        seurat_object = s_small,
        cluster_col = "res.1",
        var_genes_only = TRUE
    )
    ref[1:3, 1:3]

[Package clustifyr version 1.0.0 Index]