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 |