Differential Gene Expression (DGE) Analysis Utility Toolkit

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Documentation for package ‘DGEobj.utils’ version 1.0.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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