average_clusters {clustifyr} | R Documentation

## Average expression values per cluster

### Description

Average expression values per cluster

### Usage

    average_clusters(
      mat,
      metadata,
      cluster_col = "cluster",
      if_log = TRUE,
      cell_col = NULL,
      low_threshold = 0,
      method = "mean",
      output_log = TRUE,
      subclusterpower = 0,
      cut_n = NULL
    )

### Arguments

`mat` | expression matrix
`metadata` | data.frame or vector containing cluster assignments per cell. Order must match column order in supplied matrix. If a data.frame provide the cluster_col parameters.
`cluster_col` | column in metadata with cluster number
`if_log` | input data is natural log, averaging will be done on unlogged data
`cell_col` | if provided, will reorder matrix first
`low_threshold` | option to remove clusters with too few cells
`method` | whether to take mean (default), median, 10% truncated mean, or trimean
`output_log` | whether to report log results
`subclusterpower` | whether to get multiple averages per original cluster
`cut_n` | set on a limit of genes as expressed, lower ranked genes are set to 0, considered unexpressed

### Value

average expression matrix, with genes for row names, and clusters for column names

### Examples

    mat <- average_clusters(
        mat = pbmc_matrix_small,
        metadata = pbmc_meta,
        cluster_col = "classified",
        if_log = FALSE
    )
    mat[1:3, 1:3]

[Package clustifyr version 1.6.0 Index]