Man pages for msuprun/bbeaR
an R package and framework for epitope-specific antibody profiling
| bbea.changeAnnotation | Convert analytes to peptides in the bbeaR object created... |
| bbea.QC.heatmap.counts | Quality control heatmap of epitope counts |
| bbea.QC.heatmap.counts.byPlate | Quality control heatmap of epitope counts by individual plate |
| bbea.QC.Image | Plotting plate layout with sample labels. |
| bbea.QC.Samples | Quality control of samples by visualization of average counts |
| bbea.read.csv | Read Luminex data from original output file |
| bbea.read.csv.all | Read multiple Luminex CSV files |
| bbea.subset | Subset bbea object |
| binarizeMFIbySD | Retrieve binary indicator of peptide signal presence based on... |
| create.plate.db | Create plate layout |
| CullenFreyPlot | Generate a Cullen-Frey plot of median fluorescence intensity... |
| getAveragesByReps | From an expressionset, calculate replicate averages |
| getCVbyPeptide | Calculate the coefficient of variation for each peptide |
| getCVbyPeptide.MFI | Calculate the coefficient of variation for each peptide's... |
| getEnzymeCuts | Add sites of enzymatic cuts (by trypsin, pepsin, and... |
| getICCbyPeptide | Calculate the Intraclass Correlation Coefficient for each... |
| getPCAs | Principal component analysis of samples from ExpressionSet or... |
| getTopologynMFI | Generate topology dataframe |
| getTopologyPlotDB | Construct a dataframe that can be used for plotting |
| Image.Plate | For each plate in the object (binding, eset, or LuEpit),... |
| makeTopologyPlotBase | Generate topology plot |
| MFI2nMFI | Normalize mean flourescence intensity (MFI) values |
| mgsub | Multiple string substitution based on a specific pattern. |
| nMFI2Eset | Convert normalized mean fluorescence intensity values object... |
| pvcaBatchAssess.bbea | Principal Variance Component Analysis of samples from... |
| pvca.plot | Generate a Principal Variance Components Analysis (PVCA) plot |
| Run_doNetCirclePlot | Generate circle plots from lmFit |
