get_scaled_counts_bulk: Get a tibble with scaled counts using TMM

In tidybulk: Brings transcriptomics to the tidyverse

Description

Get a tibble with scaled counts using TMM

Usage

get_scaled_counts_bulk(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "TMM",
  reference_sample = NULL
)

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
method	A character string. The scaling method passed to the backend function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile")
reference_sample	A character string. The name of the reference sample. If NULL the sample with highest total read count will be selected as reference.

Value

A tibble including additional columns

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