remove_redundancy,tidybulk-method {tidybulk} | R Documentation

## remove_redundancy

### Description

remove_redundancy

### Usage

    ## S4 method for signature 'tidybulk'
    remove_redundancy(
      .data,
      .element = NULL,
      .feature = NULL,
      .abundance = NULL,
      method,
      of_samples = TRUE,
      correlation_threshold = 0.9,
      top = Inf,
      log_transform = FALSE,
      Dim_a_column = NULL,
      Dim_b_column = NULL
    )

### 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
`correlation_threshold` | A real number between 0 and 1. For correlation based calculation.
`top` | An integer. How many top genes to select for correlation based method
`log_transform` | A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)
`Dim_a_column` | A character string. For reduced_dimension based calculation. The column of one principal component
`Dim_b_column` | A character string. For reduced_dimension based calculation. The column of another principal component

### Value

A tbl object with with dropped recundant elements (e.g., samples).

[Package tidybulk version 0.99.23 Index]