Differential Gene Expression (DGE) Analysis Utility Toolkit
Convert count matrix to CPM, FPKM, FPK, or TPM
DGEobj.utils Package Overview
Extract a named column from a series of df or matrices
Apply low intensity filters to a DGEobj
Calculate R-squared for each gene fit
Build contrast matrix and calculate contrast fits
Run edgeR normalization on DGEobj
Apply Independent Hypothesis Weighting (IHW) to a list of topTable dat...
Run a power analysis on counts and design matrix
Calculate and add q-value and lFDR to dataframe
Test for surrogate variables
Run functions in a typical voom/lmFit workflow
Summarize a contrast list
Merge specified topTable df cols
Convert countsMatrix and geneLength to TPM units
Calculate TPM for a subsetted DGEobj
Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene Expression (DGE) analysis (Law (2015) <doi:10.12688/f1000research.9005.3>). The tools include both analysis work-flow and utility functions: mapping/unit conversion, count normalization, accounting for unknown covariates, and more. This is a complement/cohort to the 'DGEobj' package that provides a flexible container to manage and annotate Differential Gene Expression analysis results.