adjust_abundance-methods: Adjust transcript abundance for unwanted variation

In tidybulk: Brings transcriptomics to the tidyverse

Description

adjust_abundance() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with an edditional adjusted abundance column. This method uses scaled counts if present.

Usage

adjust_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  log_transform = TRUE,
  action = "add",
  ...
)

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

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

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

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

## S4 method for signature 'RangedSummarizedExperiment'
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

Details

\lifecycle

maturing

This function adjusts the abundance for (known) unwanted variation. At the moment just an unwanted covariate is allowed at a time using Combat (DOI: 10.1093/bioinformatics/bts034)

Underlying method: sva::ComBat(data, batch = my_batch, mod = design, prior.plots = FALSE, ...)

Value

A 'tbl' with additional columns for the adjusted counts as '<COUNT COLUMN>_adjusted'

A 'tbl' with additional columns for the adjusted counts as '<COUNT COLUMN>_adjusted'

A 'tbl' with additional columns for the adjusted counts as '<COUNT COLUMN>_adjusted'

A 'tbl' with additional columns for the adjusted counts as '<COUNT COLUMN>_adjusted'

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

cm = tidybulk::counts_mini
cm$batch = 0
cm$batch[cm$sample %in% c("SRR1740035", "SRR1740043")] = 1

res =
 cm %>%
 tidybulk(sample, transcript, count) %>% 
 identify_abundant() %>% 
	adjust_abundance(	~ condition + batch	)

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