add_scaled_counts_bulk.calcNormFactor {tidybulk} | R Documentation

## Calculate the norm factor with calcNormFactor from limma

### Description

Calculate the norm factor with calcNormFactor from limma

### Usage

    add_scaled_counts_bulk.calcNormFactor(
      .data,
      reference = NULL,
      factor_of_interest = NULL,
      minimum_counts = 10,
      minimum_proportion = 0.7,
      .sample = sample,
      .transcript = transcript,
      .abundance = count,
      method
    )

### Arguments

`.data` | A tibble
`reference` | A reference matrix, not sure if used anymore
`factor_of_interest` | The name of the column of the factor of interest
`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.
`.sample` | The name of the sample column
`.transcript` | The name of the transcript/gene column
`.abundance` | The name of the transcript/gene abundance column
`method` | A string character. The scaling method passed to the backend function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile")

### Value

A list including the filtered data frame and the normalization factors

[Package tidybulk version 0.99.23 Index]