Man pages for wenbostar/metaX
A flexible and comprehensive software for processing omics data.
| addIdentInfo | Add identification result into metaXpara object |
| addValueNorm | addValueNorm |
| autoRemoveOutlier | Automatically detect outlier samples |
| bootPLSDA | Fit predictive models for PLS-DA |
| calcAUROC | Classical univariate ROC analysis |
| calcVIP | Calculate the VIP for PLS-DA |
| center | center |
| checkPvaluePlot | checkPvaluePlot |
| checkQCPlot | checkQCPlot |
| cor.network | Differential correlation network analysis |
| createModels | Create predictive models |
| dataClean | dataClean |
| dir.case | dir.case |
| dir.ctrl | dir.ctrl |
| doQCRLSC | Using the QC samples to do the quality control-robust spline... |
| featureSelection | Feature selection and modeling |
| filterPeaks | filterPeaks |
| filterQCPeaks | filterQCPeaks |
| filterQCPeaksByCV | Filter peaks according to the RSD of peaks in QC samples |
| getPeaksTable | Get a data.frame which contained the peaksData in metaXpara |
| getTable | Get a table from a metaXpara object. |
| group.bw | group.bw |
| group.bw0 | group.bw0 |
| group.max | group.max |
| group.minfrac | group.minfrac |
| group.minsamp | group.minsamp |
| group.mzwid | group.mzwid |
| group.mzwid0 | group.mzwid0 |
| group.sleep | group.sleep |
| hasQC | Judge whether the data has QC samples |
| idres | idres |
| importDataFromMetaboAnalyst | importDataFromMetaboAnalyst |
| importDataFromQI | importDataFromQI |
| importDataFromXCMS | importDataFromXCMS |
| kfold | kfold |
| makeDirectory | Create directory |
| makeMetaboAnalystInput | Export a csv file which can be used for MetaboAnalyst |
| metaboliteAnnotation | Metabolite identification |
| metaXpara-class | An S4 class to represent the parameters and data for data... |
| metaXpipe | metaXpipe |
| method | method |
| missingValueImpute | Missing value imputation |
| missValueImputeMethod | missValueImputeMethod |
| myCalcAUROC | Classical univariate ROC analysis |
| myPLSDA | Perform PLS-DA analysis |
| ncomp | ncomp |
| normalize | Normalisation of peak intensity |
| nperm | nperm |
| oplsDAPara-class | An S4 class to represent the parameters for OPLS-DA analysis |
| outdir | outdir |
| pathwayAnalysis | Pathway analysis |
| peakFinder | Peak detection by using XCMS package |
| peaksData | peaksData |
| peakStat | Do the univariate and multivariate statistical analysis |
| permutePLSDA | permutePLSDA |
| plotCorHeatmap | Plot correlation heatmap |
| plotCV | Plot the CV distribution of peaks in each group |
| plotHeatMap | Plot heatmap |
| plotIntDistr | Plot the distribution of the peaks intensity |
| plotLoading | Plot figures for PCA/PLS-DA loadings |
| plotMissValue | Plot missing value distribution |
| plotNetwork | Plot correlation network map |
| plotPCA | Performa PCA analysis and plot PCA figure |
| plotPeakBox | Plot boxplot for each feature |
| plotPeakMeanDist | Plot the average peak intensity distribution |
| plotPeakNumber | Plot the distribution of the peaks number |
| plotPeakSN | Plot the distribution of the peaks S/N |
| plotPeakSumDist | Plot the total peak intensity distribution |
| plotPLSDA | Plot PLS-DA figure |
| plotQC | Plot the correlation change of the QC samples. |
| plotQCRLSC | Plot figures for QC-RLSC |
| plotROC | Perform biomarker analysis and plot ROC curve |
| plotTIC | Plot chromatogram of total ion count |
| plotTreeMap | Plot Phylogenies for samples |
| plsDAPara-class | An S4 class to represent the parameters for PLS-DA analysis |
| powerAnalyst | Power Analysis |
| prefix | prefix |
| preProcess | Pre-Processing |
| qcRlscSpan | qcRlscSpan |
| ratioPairs | ratioPairs |
| rawPeaks | rawPeaks |
| removeSample | Remove samples from the metaXpara object |
| reSetPeaksData | reSetPeaksData. Please note NA is converted to zero in... |
| retcor.method | retcor.method |
| retcor.plottype | retcor.plottype |
| retcor.profStep | retcor.profStep |
| runOPLSDA | run OPLS-DA |
| runPLSDA | runPLSDA |
| sampleListFile | sampleListFile |
| scale | scale |
| selectBestComponent | Select the best component for PLS-DA |
| svrNormalize | Batch correction using SVR normalization |
| t | t |
| transformation | Data transformation |
| validation | validation |
| xcmsSet.fitgauss | xcmsSet.fitgauss |
| xcmsSet.fwhm | xcmsSet.fwhm |
| xcmsSet.integrate | xcmsSet.integrate |
| xcmsSet.max | xcmsSet.max |
| xcmsSet.method | xcmsSet.method |
| xcmsSet.mzCenterFun | xcmsSet.mzCenterFun |
| xcmsSet.mzdiff | xcmsSet.mzdiff |
| xcmsSet.noise | xcmsSet.noise |
| xcmsSet.nSlaves | xcmsSet.nSlaves |
| xcmsSetObj | xcmsSetObj |
| xcmsSet.peakwidth | xcmsSet.peakwidth |
| xcmsSet.polarity | xcmsSet.polarity |
| xcmsSet.ppm | xcmsSet.ppm |
| xcmsSet.prefilter | xcmsSet.prefilter |
| xcmsSet.profparam | xcmsSet.profparam |
| xcmsSet.sleep | xcmsSet.sleep |
| xcmsSet.snthresh | xcmsSet.snthresh |
| xcmsSet.step | xcmsSet.step |
| xcmsSet.verbose.columns | xcmsSet.verbose.columns |
| zero2NA | Convert the value <=0 to NA |
