Man pages for peterblattmann/SWATH2stats
Transform and Filter SWATH Data for Statistical Packages
| add_genesymbol | Adds gene symbols to a table |
| assess_decoy_rate | Assess decoy rate in data |
| assess_fdr_byrun | Assess assay, peptide and protein level FDR by run (for each... |
| assess_fdr_overall | Assess overall FDR in annotated OpenSWATH/pyProphet output... |
| convert4aLFQ | Convert table into the format expected by aLFQ. |
| convert4mapDIA | Convert table into the format for mapDIA |
| convert4MSstats | Get data ready for use by MSstats. |
| convert4PECA | Convert table into the format for ROPECA |
| convert4pythonscript | Convert data into the format for running a python script. |
| convert_protein_ids | Convert protein ids |
| count_analytes | Counts the analytes across the different injections |
| disaggregate | Transforms the SWATH data from a peptide- to a... |
| filter_all_peptides | Select all proteins that are supported by peptides. |
| filter_mscore | Filter OpenSWATH output table based on mscore. |
| filter_mscore_condition | Filter OpenSWATH output table according to mscore and... |
| filter_mscore_fdr | Filter annotated OpenSWATH/pyProphet output table to achieve... |
| filter_mscore_freqobs | Filter OpenSWATH output table according to mscore. |
| filter_on_max_peptides | Filter only for the highest intense peptides |
| filter_on_min_peptides | Filter openSWATH output for proteins that are identified by a... |
| filter_proteotypic_peptides | Filter for proteins that are supported by proteotypic... |
| import_data | Transforms the column names from a data frame to the required... |
| JPP_update | Select alternate m_score column in JPP data and avert user |
| load_mart | Establish connection to biomaRt database |
| mscore4assayfdr | Find m_score cutoff to reach a desired FDR on assay level... |
| mscore4pepfdr | Find m_score cutoff to reach a desired FDR on peptide level... |
| mscore4protfdr | Find m_score cutoff to reach a desired FDR on protein level... |
| MSstats_data | Testing dataset in MSstats format. |
| OpenSWATH_data | Testing dataset from OpenSWATH. |
| plot_correlation_between_samples | Plots the correlation between injections. |
| plot.fdr_cube | S3 plot function for FDR assessment result arrays |
| plot.fdr_table | S3 plot function for results of class "fdr_table" as produced... |
| plot_variation | Plots the coefficient of variation for different replicates. |
| plot_variation_vs_total | Plots the total variation versus variation within replicates |
| reduce_OpenSWATH_output | Reduce columns of OpenSWATH data |
| removeDecoyProteins | Removes decoy proteins from the protein group label |
| rmDecoyProt | Subfunction to remove decoys |
| sample_annotation | Annotate the SWATH data with the sample information |
| Spyogenes | S.pyogenes example data. |
| Study_design | A table containing the meta-data defining the study design of... |
| transform_MSstats_OpenSWATH | Transforms column names to OpenSWATH column names |
| unifyProteinGroupLabels | Unify the protein group labels. |
| validate_columns | Validate columns for a data.frame |
| write_matrix_peptides | Writes out an overview matrix of peptides mapping to a FDR... |
| write_matrix_proteins | Writes out an overview matrix of summed signals per protein... |
