Man pages for protViz/SRMService
Report Quantitative Mass Spectrometry Data
| Annotation | Condition Map |
| annotationColumns | Annotation Columns |
| contrasts.fit.NA | version of limma::contrast.fit which is able to handle NA's... |
| correlatedPeptideList | List with peptide intensities |
| eb.fit | fit limma |
| fgcz_render_One2OneReport | perform rendering |
| fix_PD_inputFiles | massage PD inputFiles.txt - remove columns and fix column... |
| fixScaffoldQuantReport | fix scaffold file (utility function) |
| genericQuantMatrixGRP2 | Grp2Analysis reference class for running 2 grp analysis |
| getConditionColumns | get required columns for analysis |
| getIDLabels | id lables for piw |
| getIntensities | extracts Intensity columns |
| getPVals | get topTables for all coefficients from a limma lmfit ebayes... |
| getRequiredColumns | get required columns for analysis |
| Grp2Analysis-class | Perform 2 group analysis with visualization |
| grp2PullDownExample | Grp2Analysis on pulldown data example |
| mergeLimmEBayesResult | merges results produced by multigroupEBaysQvalue |
| mqQuantMatrixGRP2 | Grp2Analysis on of nockout with missing data |
| MQtoMSstatsFormat | MaxQtoMSstatsFormat |
| MSstatsMapping | mapping of MSStats file names |
| multigroupEBaysQvalue | runs limma and computes qvalues |
| PeptideTable-class | Peptide table |
| piwotPiw | piwots light |
| plotNicely | Make nice plots of transitions or peptides with correlations |
| proteinColumns | Protein Columns |
| ProteinTable-class | Protein Table |
| ProteinTableR6 | Protein Table |
| ProteinVariableSelect | Wraps 4 column matrix, with Condition, Run, Protein,... |
| QCProteinReport-class | Perform 2 group analysis with visualization |
| remap_PD_ProteinTable | remap pd proteins to format compatible with grp2Analysis... |
| RMD_LibraryGen_specLProzor | Copies the RMD and Run R file for Library generation your... |
| RMD_MQ_Quant_2GrpAnalysis | copies the RMD and Run files for 2 grp analysis based on MQ... |
| RMD_MQ_Quant_QCReport | copies the RMD and Run files for the QuantQCReport in your... |
| RMD_PD_Quant_2GrpAnalysis | copies the RMD and Run files for 2 grp analysis based on a PD... |
| RMD_QC1To1_Old | Copies the Rnw file and Run R file for old 1To1 QC into your... |
| RMD_SRM_QC_Normalization | Copies the Rnw file and Run R file for the SRM QC and... |
| RMD_VarSelection | Copies the RMD and Run files for variable selection into your... |
| SRMService-class | R access to Bibliospec File |
| transitionCorrelations | Compute correlation matrix |
| transitionCorrelationsJack | Compute correlation matrix with jack |
| TransitionTable-class | Transition table |
