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,
  .sample = sample,
  .transcript = transcript,
  .abundance = count,
  method
)

Arguments

.data

A tibble

reference

A reference matrix, not sure if used anymore

.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 1.2.1 Index]