adjust_abundance,SummarizedExperiment-method {tidybulk}R Documentation

adjust_abundance

Description

adjust_abundance

Usage

## S4 method for signature 'SummarizedExperiment'
adjust_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  log_transform = TRUE,
  action = "add",
  ...
)

Arguments

.data

A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

.formula

A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_intrest + 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)

action

A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).

...

Further parameters passed to the function sva::ComBat

Value

A 'SummarizedExperiment' object

[Package tidybulk version 0.99.23 Index]