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,
      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)
`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 0.99.23 Index]