get_adjusted_counts_for_unwanted_variation_bulk {tidybulk}R Documentation

Get adjusted count for some batch effect

Description

Get adjusted count for some batch effect

Usage

get_adjusted_counts_for_unwanted_variation_bulk(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  log_transform = TRUE,
  ...
)

Arguments

.data

A tibble

.formula

a formula with no response variable, of the kind ~ factor_of_interest + batch

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

log_transform

A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)

...

Further parameters passed to the function sva::ComBat

Value

A tibble with adjusted counts


[Package tidybulk version 1.2.1 Index]