keep_variable {tidybulk} | R Documentation

## Keep variable transcripts

### Description

keep_variable() takes as input 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
    )

    ## S4 method for signature 'spec_tbl_df'
    keep_variable(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      top = 500,
      log_transform = TRUE
    )

    ## S4 method for signature 'tbl_df'
    keep_variable(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      top = 500,
      log_transform = TRUE
    )

    ## S4 method for signature 'tidybulk'
    keep_variable(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      top = 500,
      log_transform = TRUE
    )

    ## S4 method for signature 'SummarizedExperiment'
    keep_variable(.data, top = 500, log_transform = TRUE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    keep_variable(.data, 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

'r lifecycle::badge("maturing")'

At the moment this function uses edgeR https://doi.org/10.1093/bioinformatics/btp616

### Value

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

Underlying method: s <- rowMeans((x - rowMeans(x)) ^ 2) o <- order(s, decreasing = TRUE) x <- x[o[1L:top], , drop = FALSE] variable_trancripts = rownames(x)

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

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

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

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

### Examples

    	keep_variable(
    	tidybulk::se_mini,
    	    top = 500
    	)

[Package tidybulk version 1.4.0 Index]