Man pages for VoisinneG/InteRact
Analysis of affinity purification/tandem MS data
| analyse_interactome | Construct an interactome by comparing bait and control... |
| append_annotations | Append annotations to an 'InteRactome' |
| append_FDR | Append a FDR column to an 'InteRactome' |
| append_PPI | Append protein-protein interaction |
| average_technical_replicates | Average protein intensities over technical replicates |
| compare_stoichio | Compare stoichiometries or intensities between conditions... |
| compute_correlations | Compute correlation in protein recruitment |
| compute_FDR_from_asymmetry | Compute the FDR from the asymmetry of the volcano plot |
| discretize_values | Discretize values in a vector based on a finite set of values |
| dot_plot | Dot plot representation of matrices |
| estimate_Npep | Get the number of theoretically observable peptides per... |
| filter_conditions | Filter conditions from an interactome |
| filter_Proteins | Filtering of a data frame using a threshold on protein... |
| format_axis_log10 | Generate axis breaks and labels most suitable for log10... |
| geom_mean | Perform the geometric mean of a numeric vector |
| global_analysis | Adds global variables by analysing values across all... |
| identify_conditions | Identify conditions (background, time of stimulation,... |
| identify_indirect_interactions | Identify indirect interactions by comparing stoichiometries... |
| identify_interactors | Identify specific interactors in an 'InteRactome' |
| InteRact | Analysis of AP-MS data |
| Interactome_Cbl | An example Interactome computed from the 'proteinGroups_Cbl'... |
| mean_analysis | Compute the mean 'InteRactome' (on variables 'p_val',... |
| merge_conditions | Merge different conditions from different interactomes into a... |
| merge_duplicate_groups | Merge protein groups with the same gene name. |
| merge_proteome | Add protein abundance to an 'InteRactome' |
| moving_average | Performs a running average on a numeric vector |
| normalize_interactome | Normalize the log fold change by its standard deviation for... |
| order_interactome | Order proteins within an 'InteRactome' |
| plot_2D_stoichio | Plot abundance versus interaction stoichiometries |
| plot_comparison | Plot protein intensities per biological replicate and... |
| plot_correlation_network | Plot an interactive correlation network with communities... |
| plot_density | Plot points with density background with correlation... |
| plot_FDR_map | Plot FDR as a function of parameters used to divide the... |
| plot_indirect_interactions | Plot indirect interactions |
| plot_per_condition | Dot plot representation of interaction as a function of... |
| plot_QC | Quality check plots for preprocessed AP-MS data |
| plot_stoichio | Plot interaction stoichiometries per biological replicate |
| plot_volcanos | Plot protein enrichement fold-change versus p-value |
| preprocess_data | Preprocessing of raw data |
| proteinGroups_Cbl | Characterization of protein groups identified from AP-MS data... |
| rescale_median | Normalize data frame by columns using the median |
| restrict_network_degree | Limit the number of edges per node within a network |
| row_mean | Compute the mean by row |
| row_sd | Compute the standard deviation by row |
| row_stoichio | Compute the stoichiometry of interaction using the method... |
| row_ttest | Perform a Welch two-sided t-test comparison between two... |
| smooth_interactome | Smooth, using a moving average across conditions, selected... |
| summary_protein | Create a summary for selected proteins in an 'InteRactome' |
| summary_table | Create a summary table for an 'InteRactome' |
