Man pages for jasenfinch/OrbiFIEmisc
Miscellaneous functions for the analysis of FIE-HRMS data.
| accMass | Collect accurate masses(5dp) for a given list of explanatory... |
| accMassFinal | Make final accurate mass matrix from acc_mat using the most... |
| bordaCount | Borda count of explanatory feature lists. |
| boxLinePlot | boxLinePlot |
| boxPlot | boxPlot |
| Classification | Classification |
| colExpMasses | collate all explanatory masses present in all lists. |
| corBas | corBas |
| corFeatures | correlation dendrogram of explanatory features based on all... |
| corrAnalysis | corrAnalysis |
| corVec | corVec |
| featRank | featRank |
| featSelection | featSelection |
| featTab | featTab |
| hcaPlot | hcaPlot |
| heatmapRatios | Plot heatmap of log2 ratios treatments |
| lda3d | lda3d |
| ldaDotplot | Eigenvalue dotplot using ggplot2 |
| ldaLoadings | ldaLoadings |
| ldAnalysis | wrapper function for LDA plotting, returns a list containg... |
| ldaPlots | LDA plots using ggplot2 |
| ldaStrip | Two class LDA plot using ggplot2 |
| linePlot | linePlot |
| listsOrder | Order importance scores of feature lists |
| listsPrep | listsPrep |
| listsPrepSig | return lists of explanatory masses for each pairwise |
| listsSig | Choose only significant features. |
| listsSpec | Select specific feature lists |
| logRatio | logRatio |
| masterMat | to build mean intensity matrices by class including nominal... |
| masterMix | Build mean intensity matrices by class. |
| meanShift | meanShift |
| mfs | mfs |
| occDrop | Class occupancy filtering. |
| occMat | builds occupancy matrix by class |
| outDet | changed so that actual sample labels used |
| outlierDet | outlierDet |
| pca3d | pca3d |
| pcaComp | pcaComp |
| pcaDotplot | PCA variance dotplot using ggplot2 |
| pcaLoadings | pcaLoadings |
| pcAnalysis | wrapper function for principle component analysis, returns a... |
| pcaPlots | pca plots using ggplot2 |
| plotBin | Plot peak intensities for a 2dp mass bins for all classes |
| preProc | FIE-HRMS data pre-processing |
| preProcess | preProcess |
| preprocSD | preprocSD |
| processDat | processDat |
| reFormatClassi | reFormatClassi |
| removeSig | removeSig |
| rfImportance | function to plot RF importance curves |
| runClassification | runClassification |
| saveTab | saveTab |
| scaleSS | to scale a vector to its sum of squares |
| selectionFrequencyFPR | false positive approximation for random forest selection... |
| selectMethod | pick out individual method from agg feature lists |
| shrinkList | shrinkList |
| summaryDat | summaryDat |
| TICnorm | Total Ion Count Normalisation. |
| unList | unList |
| viewSpectrum | view zoom able spectrum. double click to zoom out. 2 single... |
