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",
      test_above_log2_fold_change = NULL,
      scaling_method = "TMM",
      omit_contrast_in_colnames = FALSE,
      prefix = "",
      .sample_total_read_count = NULL
    )

### 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)
`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.
`.sample_total_read_count` |

### Value

A tibble with edgeR results

[Package tidybulk version 1.4.0 Index]