scale_abundance {tidybulk} | R Documentation

## Scale the counts of transcripts/genes

### Description

scale_abundance() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and Scales transcript abundance compansating for sequencing depth (e.g., with TMM algorithm, Robinson and Oshlack doi.org/10.1186/gb-2010-11-3-r25).

### Usage

    scale_abundance(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      method = "TMM",
      reference_sample = NULL,
      action = "add",
      reference_selection_function = NULL
    )

    ## S4 method for signature 'spec_tbl_df'
    scale_abundance(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      method = "TMM",
      reference_sample = NULL,
      action = "add",
      reference_selection_function = NULL
    )

    ## S4 method for signature 'tbl_df'
    scale_abundance(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      method = "TMM",
      reference_sample = NULL,
      action = "add",
      reference_selection_function = NULL
    )

    ## S4 method for signature 'tidybulk'
    scale_abundance(
      .data,
      .sample = NULL,
      .transcript = NULL,
      .abundance = NULL,
      method = "TMM",
      reference_sample = NULL,
      action = "add",
      reference_selection_function = NULL
    )

    ## S4 method for signature 'SummarizedExperiment'
    scale_abundance(.data, method = "TMM", reference_sample = NULL)

    ## S4 method for signature 'RangedSummarizedExperiment'
    scale_abundance(.data, method = "TMM", reference_sample = NULL)

### 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
`method` | A character string. The scaling method passed to the back-end function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile")
`reference_sample` | A character string. The name of the reference sample. If NULL the sample with highest total read count will be selected as reference.
`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.
`reference_selection_function` | DEPRECATED. please use reference_sample.

### Details

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

Scales transcript abundance compensating for sequencing depth (e.g., with TMM algorithm, Robinson and Oshlack doi.org/10.1186/gb-2010-11-3-r25). Lowly transcribed transcripts/genes (defined with minimum_counts and minimum_proportion parameters) are filtered out from the scaling procedure. The scaling inference is then applied back to all unfiltered data.

Underlying method edgeR::calcNormFactors(.data, method = c("TMM","TMMwsp","RLE","upperquartile"))

### Value

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

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

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

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

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

### Examples

     tidybulk::se_mini %>%
       identify_abundant() %>%
       scale_abundance()

[Package tidybulk version 1.4.0 Index]