keep_variable {tidybulk} | R Documentation

## Filter variable transcripts

### Description

keep_variable() takes as imput a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with additional columns for the statistics from the hypothesis test.

### Usage

    keep_variable(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      top = 500,
      log_transform = TRUE
    )

### Arguments

`.data` | A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
`.sample` | The name of the sample column
`.transcript` | The name of the transcript/gene column
`.abundance` | The name of the transcript/gene abundance column
`top` | Integer. Number of top transcript to consider
`log_transform` | A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)

### Details

At the moment this function uses edgeR only, but other inference algorithms will be added in the near future.

### Value

A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

### Examples

    	keep_variable(
    	tidybulk::counts_mini,
    	    sample,
    	    transcript,
    	    `count`,
    	    top = 500
    	)

[Package tidybulk version 0.99.23 Index]