keep_abundant,tidybulk-method {tidybulk} | R Documentation

## keep_abundant

### Description

keep_abundant

### Usage

    ## S4 method for signature 'tidybulk'
    keep_abundant(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      factor_of_interest = NULL,
      minimum_counts = 10,
      minimum_proportion = 0.7
    )

### 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
`factor_of_interest` | The name of the column of the factor of interest. This is used for defining sample groups for the filtering process.
`minimum_counts` | A real positive number. It is the threshold of count per million that is used to filter transcripts/genes out from the scaling procedure.
`minimum_proportion` | A real positive number between 0 and 1. It is the threshold of proportion of samples for each transcripts/genes that have to be characterised by a cmp bigger than the threshold to be included for scaling procedure.

### Value

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

[Package tidybulk version 0.99.23 Index]