Man pages for MassDynamics/MassExpression
MassExpression
| computeImputedCounts | Count the number of imputed features by condition and write... |
| compute_pcas | Compute PCAs |
| computeReplicateCounts | Count the replicates in each condition and write to wide... |
| createCompleteIntensityExperiment | Adds 'longIntensityDT' information to 'IntensityExperiment'... |
| createSummarizedExperiment | This function creates a summarized experiment object from a... |
| fragpipe_data | Fragpipe LFQ |
| generate_qc_report | Generate QC report |
| generate_separate_qc_reports | Generate separate QC reports |
| get_names_qc | QC plots names |
| imputeLFQ | This function does MNAR imputation |
| initialiseLongIntensityDT | This function performs the log2 conversion for intensities... |
| limmaStatsFun | This function performs the differential expression analysis... |
| listComparisonExperiments | This function creates a list of intensity experiments... |
| makeRLEBoxplotInteractive | Convert output of 'plot_rle_boxplot' to interactive |
| MassExpressionTOProtCountV2 | MassExpression output to MassDynamics V2 Protein Counts JSON |
| mq_lfq_data | MaxQuant LFQ |
| normaliseIntensity | This function normalises (based on 'normalisationMethod') the... |
| oneGroupReplDataV2 | Transform data for one protein from a long format to the... |
| oneProteinReplData | Transform data for one protein from a long format to the... |
| pd_iPRG_data | Proteome Discoverer LFQ |
| plot_chosen_pca_experiment | Plot principal components |
| plot_condition_cv_distribution | CV distributuions of a protein summarized by condition of... |
| plot_consistent_proteins_by_replicate | Lollipop plot of the number of proteins identified across all... |
| plot_density_distr | Density distribution of intensity values |
| plot_imputed_vs_not | Distribution of imputed versus non imputed values. |
| plot_log_measurement_boxplot | Boxplot of log expression values across samples. |
| plot_ma | MA plot of results |
| plot_mds_experiment | Plot first 2 dimensions of Multi-Dimensional Scaling plot |
| plot_missingness_heatmap | Heatmap showing pattern of missingness |
| plot_n_identified_proteins_by_replicate | Lollipop plot of the number of proteins identified by... |
| plot_pca_experiment | Plot first 2 dimensions of PCA |
| plot_protein_missingness | Histogram of the distribution of missingness by protein |
| plot_replicate_measured_values | Lollipop plot of missingness by intensity column |
| plot_rle_boxplot | Boxplot of the relative log expression (RLE) values across... |
| plot_samples_correlation_matrix | Correlation plot of samples using DE proteins |
| plot_volcano | Volcano plot of results |
| prepareForFiltering | Filter protein IDs that are not present in at least one... |
| preparePlottingData | Extract intensity and design from a SummarizedExperiment... |
| runGenericDiscovery | This function orchestrates the MassExpression workflow (could... |
| runLimmaPipeline | This function orchestrates imputation, normalization and the... |
| sanitize_strings | Sanitize strings for export |
| sanitize_strings_in_dataframe | Sanitize strings in dataframe |
| saveOutput | Save RData with SummarizedExperiment object and ProteinViz... |
| select_features_for_pca | Subset features to be used for PCA |
| SEToLongDT | This function converts the assay data in a protein intensity... |
| writeLimmaStatisticsTable | Write limma statistics for users to read |
| writeOutputFile | Generic function to write 'data' to 'outputFolder' with... |
| writeProteinQuantIntensities | Save txt file with differential expression analysis results... |
| writeProteinViz | This function writes a protein viz object which can be passed... |
| writeReplicateData | Write data needed for the Replicates tab This is a wrapper of... |
| writeReplicateDataV2 | Write protein_counts_and_intensity.json This is a wrapper of... |
