add_scaled_counts_bulk.calcNormFactor: Calculate the norm factor with calcNormFactor from limma

In tidybulk: Brings transcriptomics to the tidyverse

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

tidybulk documentation built on April 7, 2021, 6 p.m.