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 1.0.2 Index]