quantile_normalise_abundance-methods: Normalise by quantiles the counts of transcripts/genes

In stemangiola/tidyBulk: Brings transcriptomics to the tidyverse

Normalise by quantiles the counts of transcripts/genes

Description

quantile_normalise_abundance() takes as input A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and Scales transcript abundance compansating for sequencing depth (e.g., with TMM algorithm, Robinson and Oshlack doi.org/10.1186/gb-2010-11-3-r25).

Usage

quantile_normalise_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "limma_normalize_quantiles",
  action = "add"
)

## S4 method for signature 'spec_tbl_df'
quantile_normalise_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "limma_normalize_quantiles",
  action = "add"
)

## S4 method for signature 'tbl_df'
quantile_normalise_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "limma_normalize_quantiles",
  action = "add"
)

## S4 method for signature 'tidybulk'
quantile_normalise_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "limma_normalize_quantiles",
  action = "add"
)

## S4 method for signature 'SummarizedExperiment'
quantile_normalise_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "limma_normalize_quantiles",
  action = NULL
)

## S4 method for signature 'RangedSummarizedExperiment'
quantile_normalise_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "limma_normalize_quantiles",
  action = NULL
)

Arguments

.data	A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
.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. Either "limma_normalize_quantiles" for limma::normalizeQuantiles or "preprocesscore_normalize_quantiles_use_target" for preprocessCore::normalize.quantiles.use.target for large-scale dataset, where limmma could not be compatible.
action	A character string between "add" (default) and "only". "add" joins the new information to the input tbl (default), "only" return a non-redundant tbl with the just new information.

Details

'r lifecycle::badge("maturing")'

Scales transcript abundance compensating for sequencing depth (e.g., with TMM algorithm, Robinson and Oshlack doi.org/10.1186/gb-2010-11-3-r25). Lowly transcribed transcripts/genes (defined with minimum_counts and minimum_proportion parameters) are filtered out from the scaling procedure. The scaling inference is then applied back to all unfiltered data.

Underlying method edgeR::calcNormFactors(.data, method = c("TMM","TMMwsp","RLE","upperquartile"))

Value

A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'

A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'

A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'

A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

 tidybulk::se_mini |>
   quantile_normalise_abundance()

stemangiola/tidyBulk documentation built on April 13, 2024, 8:13 a.m.