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
