Man pages for DGEobj.utils
Differential Gene Expression (DGE) Analysis Utility Toolkit
| convertCounts | Convert count matrix to CPM, FPKM, FPK, or TPM |
| DGEobj.utils-package | DGEobj.utils Package Overview |
| 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... |
| 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 |
