R: Differential Gene Expression (DGE) Analysis Utility Toolkit

# Differential Gene Expression (DGE) Analysis Utility Toolkit

## Documentation for package ‘DGEobj.utils’ version 1.0.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DGEobj.utils-package | DGEobj.utils Package Overview
convertCounts | Convert count matrix to CPM, FPKM, FPK, or TPM
extractCol | Extract a named column from a series of df or matrices
lowIntFilter | Apply low intensity filters to a DGEobj
rsqCalc | Calculate R-squared for each gene fit
runContrasts | Build contrast matrix and calculate contrast fits
runEdgeRNorm | Run edgeR normalization on DGEobj
runIHW | Apply Independent Hypothesis Weighting (IHW) to a list of topTable dataframes
runPower | Run a power analysis on counts and design matrix
runQvalue | Calculate and add q-value and lFDR to dataframe
runSVA | Test for surrogate variables
runVoom | Run functions in a typical voom/lmFit workflow
summarizeSigCounts | Summarize a contrast list
topTable.merge | Merge specified topTable df cols
tpm.direct | Convert countsMatrix and geneLength to TPM units
tpm.on.subset | Calculate TPM for a subsetted DGEobj