scale_abundance {tidybulk}R Documentation

Scale the counts of transcripts/genes

Description

scale_abundance() takes as imput 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,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7,
  method = "TMM",
  reference_selection_function = median,
  action = "add"
)

## S4 method for signature 'spec_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"
)

## 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"
)

## S4 method for signature 'tidybulk'
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"
)

## S4 method for signature 'SummarizedExperiment'
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"
)

## S4 method for signature 'RangedSummarizedExperiment'
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.

Details

Maturing lifecycle

Scales transcript abundance compansating 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.

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



 scale_abundance(tidybulk::counts_mini,  sample, transcript, `count`)




[Package tidybulk version 1.0.2 Index]