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]