get_differential_transcript_abundance_bulk {tidybulk}R Documentation

Get differential transcription information to a tibble using edgeR.

Description

Get differential transcription information to a tibble using edgeR.

Usage

get_differential_transcript_abundance_bulk(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  .contrasts = NULL,
  method = "edgeR_quasi_likelihood",
  significance_threshold = 0.05,
  minimum_counts = 10,
  minimum_proportion = 0.7,
  fill_missing_values = FALSE,
  scaling_method = "TMM",
  omit_contrast_in_colnames = FALSE
)

Arguments

.data

A tibble

.formula

a formula with no response variable, referring only to numeric variables

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

.contrasts

A character vector. See edgeR makeContrasts specification for the parameter 'contrasts'. If contrasts are not present the first covariate is the one the model is tested against (e.g., ~ factor_of_interest)

method

A string character. Either "edgeR_quasi_likelihood" (i.e., QLF), "edgeR_likelihood_ratio" (i.e., LRT)

significance_threshold

A real between 0 and 1

minimum_counts

A positive integer. Minimum counts required for at least some samples.

minimum_proportion

A real positive number between 0 and 1. It is the threshold of proportion of samples for each transcripts/genes that have to be characterised by a cmp bigger than the threshold to be included for scaling procedure.

fill_missing_values

A boolean. Whether to fill missing sample/transcript values with the median of the transcript. This is rarely needed.

scaling_method

A character string. The scaling method passed to the backend function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile")

omit_contrast_in_colnames

If just one contrast is specified you can choose to omit the contrast label in the colnames.

Value

A tibble with edgeR results


[Package tidybulk version 1.0.2 Index]