analyze.contrast: Takes in a dds DESeq2 object and extracts results for a...
In AmyOlex/RNASeqBits: Short Scripts to Support RNA-Seq Data Analysis in R

View source: R/analyze.contrast.R

analyze.contrast

R Documentation

Takes in a dds DESeq2 object and extracts results for a specific contrast.

Description

This function was build for the repetitive contrast done in the Chuck Harrell Brain Metastasis project. It takes in severla parameters, extracts results for a specified contrast, saves the data, plots and saves a MA Plot, and plots the expression values of the top DE gene. Note: this assumes the dds condition column is named "condition" and the gene_features gene symbol column is named "Gene.Symbol".

Usage

analyze.contrast(dds, control_cond, experiment_cond, gene_features,
  contrast_name = "", celltype = "", species = "unknown_species",
  date = date())