get_scaled_counts_bulk {tidybulk} | R Documentation

## Get a tibble with scaled counts using TMM

### Description

Get a tibble with scaled counts using TMM

### Usage

    get_scaled_counts_bulk(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      factor_of_interest = NULL,
      minimum_counts = 10,
      minimum_proportion = 0.7,
      method = "TMM",
      reference_selection_function = median
    )

### Arguments

`.data` | A tibble
`.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 identifying lowly abundant transcript, to be ignored for calculating scaling fators.
`minimum_counts` | A positive integer. Minimum counts required for at least some samples.
`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.
`method` | A character string. The scaling method passed to the backend function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile")
`reference_selection_function` | A function between median, mean and max

### Value

A tibble including additional columns

[Package tidybulk version 0.99.23 Index]