Differential Gene Expression (DGE) Analysis Utility Toolkit

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Documentation for package ‘DGEobj.utils’ version 1.0.3

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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