get_differential_transcript_abundance_bulk_SE {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_SE(
  .data,
  .formula,
  sample_annotation,
  .contrasts = NULL,
  method = "edgeR_quasi_likelihood",
  test_above_log2_fold_change = NULL,
  scaling_method = "TMM",
  omit_contrast_in_colnames = FALSE,
  prefix = "",
  ...
)

Arguments

.data

A tibble

.formula

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

.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)

test_above_log2_fold_change

A positive real value. This works for edgeR and limma_voom methods. It uses the 'treat' function, which tests that the difference in abundance is bigger than this threshold rather than zero https://pubmed.ncbi.nlm.nih.gov/19176553.

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 1.5.0 Index]