| add_contrast | Create a contrast for differential expression analysis |
| add_protein_prettyprint_label | add short prettyprint labels to a protein tibble using gene... |
| adjust_modes | scale sample k by scaling factor s_k ->> don't have to... |
| aggregate_tibble_by_datatables | highly optimized aggregation of the peptides data table.... |
| analysis_quickstart | Quickstart for analyses in this pipeline |
| append_log | This function is called throughout the pipeline to append... |
| append_log_error | Append error object to log |
| append_log_timestamp | Append text to the log file and print to console, including a... |
| as_matrix_except_first_column | convert a wide-format data.frame to a matrix |
| assert_lme4_functional | Throw an error if lme4::lmer() cannot be executed |
| boxplot_add_text | placeholder title |
| cache_filtering_data | Cache data required for fast downstream peptide filtering |
| check_dataset_hascache | check if peptide tibble has cache |
| check_dataset_integrity | Test if the minimum set of required information is present in... |
| check_parameter_is_boolean | generic input validation; all provided arguments should be... |
| check_parameter_is_numeric | generic input validation; all provided arguments should be... |
| check_parameter_is_string | generic input validation; all provided arguments should be... |
| check_valid_tibble_peptides | data integrity checks for peptide tibble |
| check_valid_tibble_proteins | data integrity checks for protein tibble |
| check_valid_tibble_samples | data integrity checks for sample tibble |
| coefficient_of_variation | CoV computation for an array of non-log values |
| coefficient_of_variation_vectorized | fast CoV computation for all rows in a matrix of natural-log... |
| column_intensity_to_label | pretty-print label for an intensity column |
| contrast_to_samplegroups | return sample groups for a given contrast (column name in... |
| count_sep_char | Count how often commonly used separation characters occur in... |
| dataset_filter_custom | Custom dataset filtering rules that also enable one-sided... |
| dataset_transfer_peptide_properties | carries over protein_id, sequence_plain and sequence_modified... |
| dea | Differential expression analysis |
| dea_algorithms | returns all DEA functions integrated with MS-DAP |
| dea_algorithms_reserved | reserved DEA function names |
| dea_protein_background_foldchange_limits | estimate a threshold for 'significant' foldchanges from N... |
| dea_results_to_wide | convert the results from differential expression analysis... |
| dea_summary_prettyprint | prettyprint table that summarizes DEA results |
| de_deqms | Apply DEqMS to a protein-level ExpressionSet |
| de_ebayes | Apply limma::eBayes() function to a protein-level... |
| de_msempire | MS-EmpiRe implementation, a wrapper function for... |
| de_msqrob_customformula | MSqRob test function for internal use |
| de_msqrobsum_msqrob | Wrapper function for msqrob, using the implementation from... |
| diffdetect_results_to_wide | convert the results from differential detection analysis from... |
| diffdetect_summary_prettyprint | prettyprint table that summarizes differential detect results |
| differential_detect | Compare the number of peptide detection counts between groups |
| differential_detection_filter | Protein differential detection filtering using a hardcoded... |
| disambiguate_protein_table_by_gene | given some table with protein-level data, map to HGNC genes... |
| empty_protein_tibble | placeholder long-format proteins tibble with minimum set of... |
| enforce_sample_value_types | convert the data type of column in a sample metadata table to... |
| error_legacy_contrast_definitions | throw an error if has_legacy_contrast_definitions() is TRUE |
| export_peptide_abundance_matrix | Export peptide-level data to TSV files |
| export_protein_abundance_matrix | Rollup and export to protein-level TSV table, applied to all... |
| export_statistical_results | write statistical results to file |
| export_stats_genesummary | Create gene-level summary tables for your DEA and... |
| fasta_header_to_gene | extract gene symbol from fasta header string |
| fasta_header_to_id | extract the protein identifier from a fasta header |
| fasta_identifier_isdecoy | regex test if a protein identifier or fasta header is a decoy |
| fasta_id_short | extract the "short ID" from a fasta header. |
| fasta_parse_file | Read non-redundant headers from all fasta files |
| file_check | strip illegal characters from filename, then check for... |
| filename_extract_extension | extract the trailing file extension from a file or path |
| filename_strip_illegal_characters | from filename minus extension, replace illegal characters... |
| filter_dataset | Filter dataset |
| fit_t_dist_fixed_mu | use optim() to fit a t-distribution with fixed mu=0 |
| format_r_code | format a string of R code using the formatR and styler... |
| fragpipe_find_psm_files | Helper function to find psm.tsv files within a FragPipe... |
| fragpipe_map_combined_protein | Read FragPipe combined_protein.tsv table and then update all... |
| fragpipe_modification_to_instruction__legacy | THIS FUNCTION SHOULD ONLY BE USED FOR LEGACY FRAGPIPE... |
| fragpipe_modseq_compose | Reconstruct modified peptide sequences from disjoint... |
| fragpipe_parse_msstats | Parse a FragPipe MSstats.csv table |
| fragpipe_parse_psm | Parse a FragPipe psm.tsv table |
| fragpipe_parse_quant | Parse a FragPipe quant.csv table |
| fragpipe_peptideresults_to_dataset | From FragPipe peptide result table to an MS-DAP dataset |
| generate_pdf_report | Create the Quality Control report |
| get_column_intensity | prioritized selection of intensity column in a peptides... |
| get_mode | find the mode in a numeric array using the density function... |
| get_peptide_filternorm_variants | Return column names in peptide table that hold intensity... |
| get_protein_matrix | rollup peptides to protein data matrix for selected intensity... |
| get_samples_for_regression | collect the respective subset of samples for selected protein... |
| gg_color_hue | generate colours analogous to ggplot's default palette |
| ggplot_coefficient_of_variation | placeholder title |
| ggplot_coefficient_of_variation__leave_one_out | placeholder title |
| ggplot_peptide_abundances | plot peptide-level data for a single protein |
| ggplot_peptide_detect_frequency | placeholder title |
| ggplot_peptide_detect_frequency_distribution | placeholder title |
| ggplot_sample_detect_counts_barplots | placeholder title |
| ggplot_sample_detect_vs_metadata_scatterplot | compact scatterplot with color-coding captures all sample... |
| ggplot_sample_detect_vs_metadata_scatterplot_by_prop | separate plot for each metadata property |
| ggplot_split_legend | split a ggplot object into 2 ggplots; original plot minus... |
| has_legacy_contrast_definitions | test if the dataset has contrast definitions that are... |
| hgnc_add_xrefs | add hgnc_symbol and entrez/ensembl IDs if present in hgnc... |
| hgnc_lookuptable | Parse HGNC gene identifier lookup table that was downloaded... |
| idmap_symbols | helper function to match a protein table to HGNC via gene... |
| idmap_uniprotid | helper function to match a protein table to HGNC via an... |
| import_dataset_diann | Import a label-free proteomics dataset from DIA-NN |
| import_dataset_encyclopedia | Import a label-free proteomics dataset from EncyclopeDIA |
| import_dataset_fragpipe_ionquant | Import a label-free proteomics dataset from FragPipe;... |
| import_dataset_fragpipe_ionquant__legacy | THIS FUNCTION SHOULD ONLY BE USED FOR LEGACY FRAGPIPE... |
| import_dataset_fragpipe_psm_file | Alternative FragPipe workflow, operates directly on a single... |
| import_dataset_in_long_format | For advanced users: A generic function for importing data in... |
| import_dataset_maxquant_evidencetxt | Import a label-free proteomics dataset from MaxQuant |
| import_dataset_metamorpheus | Import a label-free proteomics dataset from MetaMorpheus |
| import_dataset_openms_mztab | Import a label-free DDA proteomics dataset from OpenMS,... |
| import_dataset_openswath | Import a label-free proteomics dataset from OpenSWATH |
| import_dataset_peaks | Import a label-free proteomics dataset from Peaks |
| import_dataset_proteomediscoverer_txt | Import a label-free DDA proteomics dataset from a... |
| import_dataset_skyline | Import a label-free proteomics dataset from Skyline |
| import_dataset_spectronaut | Import a label-free proteomics dataset from Spectronaut |
| import_expressionset | Import a label-free proteomics dataset from a peptide-level... |
| import_fasta | Import fasta file(s) that match your dataset. |
| import_maxquant_peptides | Import a label-free proteomics dataset from MaxQuant, using... |
| import_maxquant_proteingroups | Import peptide-to-protein mappings from MaxQuant |
| import_metamorpheus_proteingroups | placeholder title |
| import_metamorpheus_quantifiedpeaks | placeholder title |
| import_protein_metadata_from_fasta | Parse fasta files and construct a protein metadata table for... |
| import_sample_metadata | Import sample metadata from an Excel table |
| initialize_multiprocessing | To facilitate multiprocessing, create a Parallel Socket... |
| invalidate_cache | invalidate peptide tibble cache |
| is_dia_dataset | Test if the dataset contains DIA data, simply testing if the... |
| limma_fit_extract_stats | extract limma fit results |
| limma_wrapper | Perform linear regression with limma |
| log2_to_ln | convert base-log from log2 to natural log |
| logger.default | Log function that takes any string, appends it to global log... |
| log_peptide_tibble_pep_prot_counts | report number of detected precursor and plainseq, target and... |
| make_bins | bin an array and return both the bins and their metadata... |
| map_headers | robust matching of a list of desired columns to a character... |
| matrix_grouped_column_aggregate | fast grouped matrix aggregation using data.table |
| matrix_to_long | wrapper function around tidyverse's gather to convert a... |
| merge_fractionated_samples | merge fractionated samples |
| merge_proteingroups_by_gene | Merge protein identifiers that map to the same unique set of... |
| merge_replicate_samples | Merge technical replicates prior to downstream analysis |
| metadata_matrix_from_filenames | Guess experiment data from a set of filenames |
| mgi_lookuptable | Parse MGI ID mapping table table into a lookup table with... |
| minlog10 | Accept pvalues that are exactly zero as the 'best pvalue' |
| msdap-package | MS-DAP: Mass Spectrometry Downstream Analysis Pipeline for... |
| msdap_version | return msdap package version as a string |
| normalization_algorithms | returns all normalization algorithms integrated with MS-DAP |
| normalize_matrix | Normalize a numeric matrix; in MS-DAP this is typically a... |
| normalize_median | scale each sample such that median abundance values are the... |
| normalize_modebetween_protein | Given some peptide-level matrix, normalize samples using... |
| normalize_msempire | wrapper function for msEmpiRe::normalize() |
| normalize_peptide_intensity_column | Apply an array of normalization algorithms to some intensity... |
| normalize_rlr | Wrapper function for normalize_rlr_MSqRob_implementation |
| normalize_rlr_MSqRob_implementation | Robust Linear Regression (RLR) normalization as sourced from... |
| normalize_vwmb | Normalize a numerical matrix by the Variation Within, Mode... |
| norm_scales_fcmode | minimize the foldchange-mode between all columns |
| norm_scales_var | minimize variation over all rows in a numeric matrix |
| pairwise_modes | compute the mode of all sample/column pairs column pairs that... |
| parse_fragpipe_proteins_from_combined_proteins | Construct MS-DAP style protein group identifiers from a... |
| parse_fragpipe_proteins__legacy | THIS FUNCTION SHOULD ONLY BE USED FOR LEGACY FRAGPIPE... |
| path_append_and_check | append file to path, then call file_check() for validation of... |
| path_clean_slashes | regex replace back slashes and redundant forward/back-slashes... |
| path_exists | Combine path and filename, then check if filename exists.... |
| pdf_combine_chunks | combine PDF files |
| peptide_and_protein_counts_per_sample | add peptide and protein counts to samples tibble, so... |
| peptides_collapse_by_sequence | placeholder title |
| permute_ab | basic between-group permutation implementation |
| plot_abundance_distributions | placeholder title |
| plot_benchmark_volcano | placeholder title pre-define color_code and minlog10pval |
| plot_dia_cscore_histograms | placeholder title |
| plot_differential_detect | Plot differential detection results as a histogram |
| plot_foldchange_distribution_among_replicates | Plot within-group foldchange distributions to assess outlier... |
| plot_foldchanges | placeholder title |
| plot_peptide_data | plot peptide-level data |
| plot_peptide_data_by_contrast_to_pdf | plot peptide-level data |
| plot_pvalue_histogram | placeholder title |
| plot_retention_time_v2 | placeholder title |
| plot_roc | placeholder title prior to this; species %in% c("YEAST",... |
| plot_sample_pca | placeholder title for reference, standard pca (does not cope... |
| plot_sample_pca__sample_in_contrast | helper function for use-case beyond making a report using... |
| plot_true_false_positive_counts | placeholder title |
| plot_variance_explained | Plot the variance explained of sample metadata properties in... |
| plot_volcano | volcano plot for DEA results, split into 4 panels;... |
| plot_volcano_allcontrast | a simple wrapper around plot_volcano() that iterates all... |
| print_available_filtering_results | Return column names in peptide table that hold intensity... |
| print_contrasts | Print an overview of all defined contrasts and their... |
| print_dataset_summary | Print a short summary of a dataset to console |
| protein_eset_from_data | protein-level ExpressionSet from protein abundance matrix |
| proteingroup_to_idshort_lookuptable | lookup table for proteingroup identifiers (in long or short... |
| read_table_by_header_spec | Efficiently read a table based on some specification of... |
| read_textfile_compressed | Read text files as vector of lines or a table, supports... |
| reduce_ggplot_object_size | Reduce the memory footprint of ggplot objects |
| reformat_date | Recognize dates formatted as 8 consecutive integers and... |
| regex_classification | Classify an array of strings by regular expression |
| regex_rawfile_strip_extension | returns a regex string that can be used to remove extensions... |
| remove_by_charlength | remove NA, non-character and characters shorter than N from... |
| remove_contrasts | Remove all contrast definitions and respective filtering and... |
| remove_file_extension_from_path | remove a single file extension from a path or filename |
| remove_file_if_exists | remove file if exists |
| remove_proteins_by_name | Completely remove proteins, and all their peptides, that... |
| replace_inf_with_NA | fast replacement in a data.frame; infinite values to NA... |
| replace_nonfinite | fast replacement in a vector; nonfinite to target value |
| replace_zero_with_NA | fast replacement in a data.frame; zero values to NA... |
| reset_log | clear the log by resetting global log_ variable |
| rgd_lookuptable | Parse RGD ID mapping table table into a lookup table with... |
| rmarkdown_xtable_custom | placeholder title https://stackoverflow.com/a/16580525 |
| robust_header_matching | robust matching of column names to a data.frame, returns the... |
| rollup_pep2prot | wrapper function for peptide-to-protein rollup |
| rollup_pep2prot_maxlfq | rollup by MaxLFQ algorithm |
| rollup_pep2prot_summation | rollup a peptide tibble by summation of all intensity values... |
| rollup_pep2prot_tmp | rollup a peptide tibble by applying Tukey's median polish... |
| sample_color_coding | generate color-coding for all sample metadata |
| sample_color_coding__long_format | generate color-codings for all sample metadata |
| sample_metadata_custom | For advanced users: import sample metadata directly from the... |
| sample_metadata_from_file | read sample metadata table from file and match it against... |
| sample_metadata_from_filenames | extract metadata from sample names using regular expressions |
| sample_metadata_sort_and_filter | sample metadata formatting and validation |
| scale_between_quantiles | scale an array of numerics between 0~1, thresholding values... |
| score_classification_counts | score which classification works best when e.g. guesstimating... |
| setup_contrasts | Setup contrasts for downstream Differential Expression... |
| shift_empty | try to align matrix columns eg; inconsistent use of... |
| smooth_loess_custom | Loess fit on finite value pairs. Ignores overfit warnings,... |
| split_alt_sep_char | detect case of forgotten separation character, alternative... |
| split_array | split array into a list of N-sized chunks |
| split_char_num | detect case of forgotten separation character |
| split_generic | generic detection of metadata splitting |
| split_recursively | recursively split within all columns of a matrix |
| strip_common_substring | remove starting or trailing substrings that ar the same for... |
| subchunkify | placeholder title https://github.com/yihui/knitr/issues/1494... |
| subset_protein_eset_for_dea | helper function to double-check we don't submit an... |
| subset_relevant_code_snippet_for_report | subset lines of R code (provided as strings) from the last... |
| summarise_stats | Summarize DEA and/or differential detection results in a... |
| summarise_stats__for_contrast | worker function for actual stats summary |
| threshold_numerics | threshold finite numeric values |
| tibble_as_eset | peptide-level ExpressionSet from long-format peptide data |
| tibble_peptides_reorder | rearrange column in a long-format peptides tibble |
| update_protein_mapping | For advanced users: update a peptide tibble with new... |
| update_protein_mapping_from_maxquant | Update the peptide-to-protein mappings using a MaxQuant... |
| user_provided_metadata | Get column names that represent sample metadata provided by... |
| validate_eset_fitdata | Input validation for eBayes/DEqMS/MS-EmpiRe functions |
| write_template_for_sample_metadata | Write an Excel sheet to file that contains all samples in the... |
