Man pages for mkajano/HDXBoxeR
Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data
| all_summary | Returns full summary table. |
| arg_df | Returns initially processed data.frame from the export from... |
| arguments_call1 | Returns default arguments for the output_tp functions. States |
| arguments_call2 | Returns default arguments for the output_tp functions.... |
| arguments_call3 | Returns default arguments for the output_tp functions. #... |
| arg_UN_FD | Returns initially processed data.frame from the export from... |
| average_timecourse | Calculates average for time course data. |
| ave_timepoint | Returns average value for either uptake of procent data. |
| av_tc | Preparatory function for average plot for timecourses |
| av_tp | Preparatory function for average plot |
| backHX_calculations | Summary of backexchange summary |
| boxplot_tp | Plots boxplots for all the averages in the set |
| CI_2pts | Global confidence interval treshold from experimental... |
| CI_single | Global confidence interval treshold from experimental... |
| CI_tc | Critial interval calculation two sets of timecourses |
| CI_tp | Global confidence interval treshold from experimental... |
| color_ranges_Blue_Red_heat_map | Returns color pallete from red to blue with number of colors... |
| color_ranges_Spectral | Returns Spectral pallette with colors matching defined ranges |
| coverage_residue | Returns coverage per residue |
| deuteration_woods_timecourse | Return woods plots for the timecourse |
| deuteration_woods_timepoints | Return woods plots for the timepoints |
| dif_ave | Returns data frame with difference of averages between State1... |
| dif_tp | Preparatory function for difference plot |
| dif_tp_proc | Preparatory function for difference plot |
| duplicate_sets | Duplicate set function |
| extreme_input_gap | Makes input for Extreme for bimodal analysis. |
| extreme_input_undeut | Makes input for Extreme for bimodal analysis. |
| general_info | Provides summary table for all data.sets. |
| getCoords1 | function from plotfunctions package |
| heat_map_tc | Plots heat maps for time courses. |
| heat_map_tp | Preparatory function for heat map |
| heat_map_tp_maxuptake | Preparatory function for heat map of maximum uptake per... |
| heat_map_tp_maxuptake_proc | Preparatory function for heat map of maximum procent... |
| heat_map_tp_proc | Preparatory function for heat map for procent deuteration |
| is.nan.data.frame | Checks for NaN is data.frame |
| lab_dif | Legend for difference in averages plot. |
| lab_dif_proc | Preparatory function for difference plot for procent... |
| lab_vol | Preparatory function for volcano plot legends |
| legend_heat_map | Legend for the heatmaps prep function. |
| legend_heat_map_tc | Legend for the heatmaps for timecourses. |
| legend_heat_map_timecourse | Legend for the heatmaps prep function for timecourses. |
| legend_heat_map_tp | Legend for the heatmaps.Extracts names from data.frame |
| legend_heat_map_tp_proc | Legend for the heatmaps percent.Extracts names from... |
| legend_nm_bottom | Legend, bottom of the plots |
| legend_raw_ave | Legend for average plot. |
| legend_raw_ave_proc | Preparatory function to draw legends for average procent |
| legend_raw_ave_tc | Legend for average deuteration plot for timecourse. |
| legend_sig_peptides | Legend for the significant peptides |
| legend_states_PerD_bottom | Legend, bottom of the plots |
| legend_tc_bottom | Preparatory function returns legends for the timecourses. |
| nm_states | Lists names of states in data sets |
| output_FD | Prepares output for HDX-MS Full deuteration data |
| output_FD_proc | Prepares output for HDX-MS Full deuteration data for procent... |
| output_prep | Prepares output with HDX-MS data for publications |
| output_tc | Prepares output for HDX-MS for the deuteration uptake or... |
| output_tp | Prepares output for HDX-MS for the deuteration uptake or... |
| output_UD | Prepares output for HDX-MS Undeuterated sample data. |
| output_UD_proc | Prepares output for HDX-MS Undeuterated data for procent... |
| pallette_legend | Color scheme using heatmap. Legend Extracts names from... |
| pallette_ll | Color scheme using heatmap. Legend extracts names from data... |
| peptide_pv_tp | Preparatory function for significant peptide plots |
| peptide_pv_tp_proc | Preparatory function for showing peptides with significant... |
| pl_gen_ch2 | Prepares the plot window for the woods functions |
| pl_gen_uptake | Prepares the plot window for the woods functions |
| plot_heat_map_max_uptake_tp | Plots heat maps for maximum uptake per residue. |
| plot_heat_map_max_uptake_tp_proc | Plots heat maps for maximum procent deuteration per residue. |
| plot_heat_map_tc | Plots heat maps for time courses. |
| plot_heat_map_tp | Plots heat maps for significant peptides. |
| plot_heat_map_tp_proc | Plots heat maps for significant peptides. |
| plot_peptide_sig_tp | Significant peptide plots. |
| plot_peptide_sig_tp_proc | Draws peptides with significant difefrences between sets. |
| plots_av_tcourse | Generates average deuteration plot for the time-course. |
| plots_av_tp | Returns average deuteration plot for timepoints in the data... |
| plots_av_tp_proc | Returns average procent deuteration plot for time points |
| plots_diff_tp | Returns difference in average plot for timepoints in the data... |
| plots_diff_tp_proc | Returns difference in average procent deuteration plot for... |
| plots_vol_tp | Returns volcano plots for timepoints in the data frame |
| ppar | Preparation of figure window. |
| ppar_bottom_legend | Preparation of figure window with area for figure at the... |
| pparLM | Preparation of figure window. small margins |
| ppar_wider | Preparation of figure window with more area on west side of... |
| prep_timecourse_plot_ave | Prepares function for plotting averages in timecourse |
| prep_timecourse_plot_sd | Prepares function for Critical interval for timecourses |
| pv_timecourse | pvalue calculation between two sets of the data at certain... |
| pv_timepoint | Calculation of pvalue between first protein state and any... |
| pymol_script_average_residue | Writes a text files with pymol scripts to list significant... |
| pymol_script_significant_peptide | Writes a text files with pymol scripts to list significant... |
| pymol_script_significant_peptide_proc | Writes a text files with pymol scripts to list significant... |
| pymol_script_significant_residue | Writes a text files with pymol scripts to list significant... |
| pymol_script_significant_residue_proc | Writes a text files with pymol scripts to list significant... |
| pymol_str | Preparatory function writing pymol scripts |
| qpcr.cbind.na | Hidden function from qpcR package, typical usage as... |
| ranges_function | Gives ranges for the averages |
| ranges_function_tc | Gives ranges for the averages for time course analysis |
| rbind_na | bind non equal row |
| reset_par | Reset plotting window parameters to default |
| robot_2states_indexes | Returns a robot plot for selected peptides for 2 protein... |
| robot_indexes | Returns indexes for peptides with significant difference... |
| robot_indexes_df | Returns dataframe with peptides which exhibit significant... |
| robot_plot_All | Returns a robot plot for comparisons of the timepoints... |
| sd_timecourse | Returns standard deviation for uptake data for timecourses. |
| sd_timecourse_proc | Returns standard deviation for percent deuteration data for... |
| sd_timepoint | Returns standard deviation for dataframe. |
| select_indices | Allows for selecting some peptide from input data |
| significant_peptide_uptake | Function returns which peptides are significantly based of... |
| summary_sd_CI | Provides summary table with Critical interval and standard... |
| uptake_plots | Uptake plots |
| verbose_timecourse_output | Returns csv with averages from analysis for procent... |
| verbose_timepoint_output | Returns csv with averages from analysis for uptake file,... |
| vol_tp | Preparatory function for volcano plot |
| woods_CI_plot | Returns a woods plot for comparisons of the timepoints... |
