adjust_abundance,tbl_df-method {tidybulk} | R Documentation

## adjust_abundance

### Description

adjust_abundance

### Usage

    ## S4 method for signature 'tbl_df'
    adjust_abundance(
      .data,
      .formula,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      log_transform = TRUE,
      action = "add",
      ...
    )

### Arguments

`.data` | A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
`.formula` | A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_intrest + batch)
`.sample` | The name of the sample column
`.transcript` | The name of the transcript/gene column
`.abundance` | The name of the transcript/gene abundance 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 sva::ComBat

### Value

A 'tbl' with additional columns for the adjusted counts as '<COUNT COLUMN>_adjusted'

[Package tidybulk version 0.99.23 Index]