scale_abundance,tbl_df-method {tidybulk} | R Documentation

## scale_abundance

### Description

scale_abundance

### Usage

    ## S4 method for signature 'tbl_df'
    scale_abundance(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      factor_of_interest = NULL,
      minimum_counts = 10,
      minimum_proportion = 0.7,
      method = "TMM",
      reference_selection_function = median,
      action = "add"
    )

### 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 identifying lowly abundant transcript, to be ignored for calculating scaling fators.
`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. The scaling inference is then applied back to all unfiltered data.
`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 fucntion that is used to selecting the reference sample for scaling. It could be max (default), which choose the sample with maximum library size; or median, which chooses the sample with median library size.
`action` | A character string between "add" (default) and "only". "add" joins the new information to the input tbl (default), "only" return a non-redundant tbl with the just new information.

### Value

A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'

[Package tidybulk version 0.99.23 Index]