Man pages for scottwalmsley/wSIMCity
Searching wide SIM - wide-MS2 data (DIA) for neutral losses
| assign_isotopes | Assign isotopes to a feature set |
| calcIsotopeMatrix | Create a matrix for isotope abundanc computation and id |
| compute_formulae | Compute molecular formulae for a list of masses in the... |
| compute_group_data | compute group statistics |
| count_peak_groups | count_peak_groups |
| create_hit_table | Create a hit table of results in the SQLite data base. |
| create_ref_table | Creates a reference / master table of compounds for RT... |
| createTables | Create tables for hit lists |
| delta_formula | Compute the delta formula for two features, the precursor and... |
| findIsotopes | Find isotopic peaks in peak data |
| findIsotopesPspec | Find isotopes in psuedo spectra |
| find_known_adducts | Find known adducts by searching against a database of known... |
| find_peaks | Find peaks from a vector of intensities |
| getAlignmentData | Get alignment data from aligned DNA adducts |
| get_atom_counts | Retrieve the atomic counts and mass defect for a given... |
| get_hit_table | Get plotly figure for table |
| getMassTolRange | getMassTolRange |
| getPeak | Get the peak |
| getValid | get valid atomic formulae |
| groupFWHM | Group peaks by retention time |
| join_align | Perform retention time aligment using the joing align... |
| list.dirs.depth.n | List directories in folder |
| mdnadb | Known modified DNA nucleotides. |
| merge_tables | Merge two sqlite DB tables together for alignment |
| naOmit | Omit NA values |
| plot_candidate | Plot candidate DNA adduct |
| plot_dna_adduct_map | Plot a DNA adduct heat map |
| plotPeak | Plots the spectrum of precursor and aglycones |
| plot_peak_group | plot peaks that are DNA adducts. |
| plotPeak.plotly | Plots the spectrum of precursor and aglycones using plotly |
| ppmErr | ppmErr |
| refine_table | Refine table and remove duplicates |
| search_delta_mass | search_delta_mass |
| search_filter | search_filter |
| search_NLM | search_NLM Wrappper function to search for the neutral loss... |
| setScanDef | set_scan_def |
| similarityScore_gauss | Score similarity using Gaussian function |
| similarityScore_laplace | Score similarity using Gaussian function |
