de_analysis: Perform Differential Expression Analysis

In luciorq/txomics: Functional Analysis and Visualization of Transcriptomic Data

Description

Run DESeq2 pipeline for differentially expressed genes.

Usage

de_analysis(tx, sample_table, contrast_var, numerator, denominator,
  batch_var = NULL, beta_prior = TRUE, force_rep = FALSE,
  parallel = FALSE)

Arguments

tx	imported transcripts object containing reads counts
sample_table	metadata data frame, containing description of each sample and experimental design
contrast_var	column name from the sample_table
numerator	factor from contrast_var to be considered as treatment
denominator	factor from contrast_var to be considered as control
batch_var	column from sample_table to be considered for batch effect
beta_prior	default = TRUE, set to FALSE to use apeglm method
force_rep	default = FALSE, experimental
parallel	Use all available cores to run. Uses significantly more RAM. Default = FALSE.

Value

A tibble object

luciorq/txomics documentation built on Sept. 3, 2020, 5:36 a.m.