cluster_elements,SummarizedExperiment-method {tidybulk} | R Documentation

## cluster_elements

### Description

cluster_elements

### Usage

    ## S4 method for signature 'SummarizedExperiment'
    cluster_elements(
      .data,
      .element = NULL,
      .feature = NULL,
      .abundance = NULL,
      method,
      of_samples = TRUE,
      log_transform = TRUE,
      action = "add",
      ...
    )

### Arguments

`.data` | A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
`.element` | The name of the element column (normally samples).
`.feature` | The name of the feature column (normally transcripts/genes)
`.abundance` | The name of the column including the numerical value the clustering is based on (normally transcript abundance)
`method` | A character string. The cluster algorithm to use, ay the moment k-means is the only algorithm included.
`of_samples` | A boolean. In case the input is a tidybulk object, it indicates Whether the element column will be sample or transcript column
`log_transform` | A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)
`action` | A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
`...` | Further parameters passed to the function kmeans

### Value

A 'SummarizedExperiment' object

[Package tidybulk version 0.99.23 Index]