Man pages for lauzikaite/massFlowR
LC-MS Data Pre-Processing
| addERRS | Add peak matching error windows using user-defined _m/z_ and... |
| alignPEAKS-massFlowTemplate-method | Align peaks detected in LC-MS samples using spectral... |
| annotateDS-massFlowAnno-method | Annotate dataset using chemical reference database. |
| assignCOS | Assign dataset's peak-groups to template peak-groups based on... |
| buildANNO | Build a 'massFlowAnno' class object. |
| buildDB | Build a chemical reference database table using rda files |
| buildGRAPH | Build a correlation network of peaks |
| buildTMP | Build a sample alignment and annotation template |
| buildVECTOR | Build a vector for a peak-group using peaks _m/z_ and... |
| checkANNOTATION-massFlowAnno-method | Check annotation results between selected database chemical... |
| checkFILE | Check and load file for peak alignment |
| cleanPEAKS | Clean peak table from duplicating peaks |
| comparePCS-massFlowAnno-method | Compare selected pseudo chemical spectra. |
| corEIC | Obtain EIC correlation between two peaks |
| corPEAKS | Correlate two peaks' intensities across all samples. |
| do_alignPEAKS | Align dataset's and template peaks using dot-product... |
| do_groupPEAKS | Group peaks of a single LC-MS spectrum using EIC correlation |
| exportPEAK | Export centWave measures for a peak-of-interest in every... |
| exportSAMPLE | Extract centWave values for peaks in the final template for a... |
| extractCOMMUNITIES | Extract communities, or, Pseudo Chemical Spectra, with > 1... |
| extractEIC | Obtain extracted ion chromatograms for all picked peaks |
| extractINT | Extract raw signal values for defined mz and rt region. |
| extractMISS | Extract samples with missed peaks, for which intensity have... |
| extractPEAKGR | Extract peak-group data from every sample |
| filepath-massFlowTemplate-method | Obtain the absolute path to metadata file of the experiment |
| fillPEAKS-massFlowTemplate-method | Fill peaks |
| fillSAMPLE | Fill intensity values for peaks missed in the... |
| findANNOchemid-massFlowAnno-method | Find annotations for selected chemical compound id |
| findANNOpcs-massFlowAnno-method | Find annotations for selected pseudo chemical spectra |
| getCORmat | Build a correlation matrix between peaks-of-interest |
| getCOSmat | Estimate cosine angles between the vectors representing... |
| getINT | Get intensity of a peak-of-interest in a single sample. |
| getMATCHES | Get template peaks that match the target peak by _m/z_ and... |
| getPEAKIDS | Extract peakids from every community/Pseudo Chemical Spectra... |
| getPEAKmedians | Get median centWave measures for a peak-of-interest across... |
| getRTbins | Split a dataset-of-interest and template into _rt_ regions... |
| groupPEAKS | Get peak-groups representing different chemical spectra in... |
| groupPEAKS_paral | Perform peak-picking and grouping into Extracted Chemical... |
| loadALIGNED | Build sample alignment and annotation template using already... |
| massFlowAnno-class | massFlowAnno, a class for peak table annotation with a... |
| massFlowR-package | massFlowR: a package for pre-processing of high-resolution,... |
| massFlowTemplate-class | massFlowTemplate, a class for sample alignment and annotation |
| modelPEAKS | Function models intensity integration values for missing... |
| normSPEC | Normalise a vector representing peaks' intensity values to... |
| orderBYrt | Order a peak table by variables' _rt_ |
| peaksVALIDATED-massFlowTemplate-method | Check if massFlowTemplate object was validated |
| pickPEAKS | Peak detection using the centWave method |
| rankCOS | Rank cosines, assigning 1 to the highest cosine and 0s to... |
| rbindCLEAN | Bind a list of data frames |
| readDATA | Read raw LC-MS data into memory |
| scaleEDGES | Scale correlation coefficients |
| smoothVALUE | Helper function to model intensity integration values for... |
| validFILE | Check the validity of a raw LC-MS file. |
| validPEAKGR | Validate a peak-group-of-interest by performing a... |
| validPEAKS-massFlowTemplate-method | Validate aligned peaks and their corresponding peak-groups |
