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,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7,
  .sample = sample,
  .transcript = transcript,
  .abundance = count,
  method
)

Arguments

.data

A tibble

reference

A reference matrix, not sure if used anymore

factor_of_interest

The name of the column of the factor of interest

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.

.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 1.0.2 Index]