get_differential_transcript_abundance_deseq2: Get differential transcription information to a tibble using...

In tidybulk: Brings transcriptomics to the tidyverse

Description

Get differential transcription information to a tibble using DESeq2

Usage

get_differential_transcript_abundance_deseq2(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  .contrasts = NULL,
  method = "edgeR_quasi_likelihood",
  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
.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)
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

tidybulk documentation built on April 7, 2021, 6 p.m.