| aa_residues | Masses of amino acid residues. |
| add_col_rawfile | Adds column 'raw_file'. |
| add_cols_at | Pads columns to a placeholder data frame. |
| add_custom_entrez | Adds custom Entrez IDs and optional overwriting species |
| add_empai | Adds column "prot_empai" |
| add_entrez | Adds Entrez IDs |
| add_entry_ids | Adds numeric indices for peptides or proteins |
| add_fasta_attrs | Helper of parse_fasta. |
| add_mascot_pepseqmod | Adds the 'pep_seq_mod' field to Mascot PSMs |
| add_mascot_raw | Adds RAW_File column |
| add_maxquant_pepseqmod | Adds the 'pep_seq_mod' field to MaxQuant PSMs |
| addMBRpeps | Add MBR peptide intensities |
| add_mbr_psms | Adds MBR PSMs from psmC |
| add_mean_dev | Adds mean-deviation |
| add_mod_conf | Adds column "pep_var_mod_conf" |
| add_msfragger_pepseqmod | Adds the 'pep_seq_mod' field to MSFragger PSMs |
| add_msgf_pepseqmod | Adds the 'pep_seq_mod' field to PSMs. |
| add_n_pepexpz | Calculates the number of unique charge states of peptides. |
| add_pep_n_apexes | Add column 'pep_n_apexes' |
| add_pep_retsd | Helper of calc_pep_retsd |
| add_pepseqmod | Adds the 'pep_seq_mod' field to PSMs. |
| add_prot_desc | Helper of parse_fasta. |
| add_prot_icover | Finds peptide abundance indexes. |
| add_psm_apexes | Add PSM apexes by each 'RAW_File'. |
| add_quality_cols | Adds columns 'pep_n_psm', 'prot_n_psm' and 'prot_n_pep'. |
| add_refseq_gene | Adds gene IDs for RefSeq |
| add_scan_id | Add 'pep_scan_id' |
| add_shared_genes | Find peptides that are shared by genes. |
| add_shared_prot_accs_mf | Finds the shared protein accessions when using MSFragger. |
| add_shared_sm_genes | Find peptides that are shared by genes. |
| add_sm_pepseqmod | Adds the 'pep_seq_mod' field to MaxQuant PSMs |
| aggrLFQs | Aggregation of LFQ intensity. |
| aggrNumLCMS | Aggregates data from the same TMT_Set at different... |
| aggrNums | Summarizes numeric values |
| aggrTopn | Sums top_n |
| alignPSMApexs | Align PSM apex retention times |
| anal_KinSub | PSP outputs of kinase-substrate interactions |
| analNMF | NMF analysis |
| anal_pepNMF | NMF Classification |
| anal_prnString | STRING outputs of protein-protein interactions |
| anal_prnTrend | Trend analysis of protein data |
| analTrend | Trend analysis |
| annot_from_to | Helper to map 'SYMBOL' to 'ENTREZID' |
| annotKin | Adds kinase annotation |
| annot_KinSub | Annotates kinase-substrate interactions |
| annotPeppos | Annotation of peptide positions and adjacent amino acid... |
| annotPrn | Adds protein annotation |
| annotPSM | Annotates PSM results |
| annot_stringdb | Annotates protein STRING ids |
| arrangers_in_call | Arranges rows |
| assign_duppeps | Assign duplicated peptides to a leading protein |
| batchPSMheader | Processes Mascot PSMs |
| byfile_gspahm | A helper function for gspaHM by input file names |
| byfile_plotVolcano | Plot volcanos |
| byfml_gspahm | A helper function for gspaHM by formula names |
| byfml_volcano | Formula specific volcano plots |
| c2_msig_hs | Entrez IDs of human molecular signatures. |
| c2_msig_mm | Entrez IDs of mouse molecular signatures. |
| c2_msig_rn | Entrez IDs of rat molecular signatures. |
| calc_avgpep | Averaged peptide molecular weight (for proteins) |
| calc_cover | Calculates protein percent coverage |
| calc_lfq_log2r | Helper: calculates LFQ log2FC. |
| calclfqPepInts | Calculates 'pep_tot_int', 'pep_razor_int' and... |
| calclfqPepNums | Calculates log2FC of peptides based on LFQ intensity. |
| calcLFQPeptide | Calculates Mzion peptide data for individual TMT experiments |
| calcLFQprnnums | Adds the 'total', 'razor' and 'unique' intensities of... |
| calc_mq_log2r | Helper of calculating MaxQuang log2FC |
| calc_pep_retsd | Calculates the standard deviation in the retention times of... |
| calc_sd_fcts | Calculates standard deviations and the corresponding factors... |
| calc_sd_fcts_psm | Calculates PSM SDs |
| calcSD_Splex | Calculates CV per TMT_Set and LCMS_injection |
| calcTMTLabs | Calculates labeling efficiency |
| calcTMTPeptide | Calculates peptide data for individual TMT experiments |
| calc_tmt_prnnums | Helper: calculates the TMT log2FC and reporter-ion intensity... |
| calibPSMApexs2 | Calibrate PSM apex retention times under 'apex_ts1' or... |
| center_df | Updates df after normalization. |
| channelInfo | Extracts the channel information in TMT experiments |
| check_aes_length | Checks lengths of aesthetics. |
| check_channel_prefix | Adds the 'TMT-' prefix. |
| check_depreciated_args | Checks depreciated arguments |
| check_dots | Checks duplicate argments in 'dots' |
| checkdots_analTrend | Check the dot-dot-dot of anal_prnTrend. |
| check_dups_at_lcms_and_sid | Checks duplicated Sample_IDs in different LCMS_Injection's... |
| check_dup_unimods | Checks duplicated 'Anywhere' variable modifications. |
| check_empty_rows | Removes rows of all NA values |
| check_exptfrac_raws | Checks the consistency in RAW_File between expt_smry.xlsx and... |
| check_formalArgs | Checks conflicts in function arguments. |
| check_formalArgs2 | Checks conflicts in function arguments. |
| check_frac_multipsms | Checks the PSM_File in frac_smry.xlsx |
| check_ggplot_aes | Checks missing values in a ggplot2 object. |
| check_gset_nms | Checks 'gset_nms' |
| check_lfq_exptraws | Checks duplicated RAW_Files in expt_smry.xlsx for LFQ. |
| check_metadata_integers | Checks the integerish of columns. |
| check_mq_df | Compare sample IDS between MaxQuant results and... |
| check_optional_cols | Checks the default columns in metadata. |
| check_raws | Finds mismatches in RAW file names |
| check_required_cols | Checks the presence of required columns in metadata. |
| check_tmt126_row | Checks the rows TMT-126 in metadata. |
| check_tmt_chans_vs_levs | Checks the consistency between TMT_Channel's and TMT_level's. |
| check_tmt_emptyids | Checks the uniqueness of Sample_ID for Empty's. |
| check_tmt_mixplexes | Checks TMT_Channel after check_channel_prefix where "126"... |
| check_tmt_nc | Standardizes TMT channel name. |
| check_tmt_plex | Standardizes TMT-plexes. |
| check_tmt_rawfiles | Checks the uniqueness of RAW_File per TMT_Set and... |
| check_tmt_ref | Checks the 'Reference' channels in metadata |
| check_tmt_sampleids | Checks the counts of Sample_ID under each TMT_Set and... |
| check_unnamed_cols | Checks the columns without names in metadata. |
| cleanPSMRT_by_sets | Clean up PSM retention times for a set of TMTset[i]LCMSinj[j] |
| cleanRTChim | Clean PSM data with multiple precursors |
| cleanupPSM | Cleans Up PSM results |
| cluego | ClueGO via API |
| cmbn_meta | Combines data with metadata |
| colAnnot | Sets up the column annotation in heat maps |
| collapse_psm_charges | Collapse PSMs at good proximity of retention times |
| compile_hdr_mods | Compiles Mascot modification indexes. |
| concat_fml_dots | Concatenates formula(s) to varargs of dots |
| contain_str | Helper of row filtration |
| cos_sim | Cosine similarity. |
| count_pepmiss | Peptide mis-cleavage counts |
| count_phosphopeps | Counts phospho. |
| create_db_path | Helper to create 'db_path' |
| create_os_lookup | create a lookup table and remove duplicated entries |
| dblTrim | Data normalization |
| deduce_mod_indexes | Deduces mod_indexes. |
| Dixon_outliers | Outlier removals with Dixon's method |
| dixon_test | Outlier removals with Dixon's method |
| dl_msig | Helper to download 'gmt' |
| env_where | Finds the environment of a function |
| extract_mq_ints | Extracts MaxQuant intensity values and calculates log2FC. |
| extract_psm_raws | Extracts the names of RAW MS files from PSM data |
| extract_raws | Extracts RAW MS file names |
| fillMFprnnums | Adds MSFragger intensity and ratio columns |
| fillMQprnnums | Adds MSFragger intensity and ratio columns |
| filterData | Filters rows by variance quantiles |
| filters_in_call | Filters rows |
| find_abbr_species | Helper to find the two-letter character string of abbreviated... |
| find_best_mbry | Find the best intensity |
| find_delim | Finds the deliminator of a file. |
| find_fit_nms | Finds sample IDS for used in the current fitting. |
| find_fn_bases | Finds the base names of files |
| find_fn_exts | Finds the extensions of files |
| find_human_orthologs | Helper to find human orthologs |
| find_int_cols | Finds the columns of reporter-ion intensity. |
| find_mascot_plex | Finds the plexes according to the Mascot outputs. |
| find_mascot_psmraws | Finds the names of Mascot PSM files. |
| find_mascot_tmtplex | Finds the TMT-plex from Mascot PSM exports |
| find_mascot_vmods | Finds the variable modifications. |
| find_mbr_int | Find the MBR intensity |
| find_mbr_ms1files | Find MBR MS1 files |
| find_mf_psmraws | Finds the names of MSFragger PSM files. |
| find_mod_indexesQ | Finds mod_indexes. |
| find_mq_psmraws | Finds the names of MaxQuant PSM files. |
| find_n_comp | Checks 'n_comp' |
| find_NorZ | Finds the patterns of log2FC columns. |
| find_padding_pos | Finds the padding positions of TMT channels. |
| find_path_ms1 | Find the path of MS1 data |
| find_pep_pos | Finds peptide start and end positions |
| find_pq_psmraws | Finds the names of proteoQ PSM files. |
| find_preceding_colnm | Helper: finds the column name before 'to_move'. |
| find_pri_df | helper for finding input 'df' |
| find_prot_family_rows | Helper: finds the row indexes of a protein within a family |
| find_psmQ_files | Finds the list of psmQ files. |
| find_ratio_cols | Finds the columns of reporter-ion ratios. |
| find_search_engine | Finds the type of search engine |
| find_sec_df | Helper for finding input 'df' (not currently used). |
| find_shared_prots | Finds peptides that are shared by proteins. |
| find_sm_psmraws | Finds the names of Spectrum Mill PSM files. |
| fitKernelDensity | Data normalization |
| fitMS1RT | Calibrate MS1 retention times |
| fixBrukerMGF | Fix the 'File' field in 'Title' lines. |
| fml2mass | Standarizes mixtured MSGF formulas and masses to monoisotopic... |
| fml_gsea | Protein GSEA by formula(s) in 'pepSig' or 'prnSig' |
| fml_gspa | Helper of GSPA. |
| fmt_num_cols | Formats numeric columns |
| fullVolcano | Volcano plots for all proteins or peptides in a data set |
| geom_lower_text | Geom plot for ggpairs |
| geom_table | Prints table in ggplot2 images |
| get_col_types | Gets column types. |
| get_full_entrez | Helper to get a complete list of 'ENTREZID' from 'egUNIPROT' |
| get_gl_dat_dir | Fetches global 'dat_dir'. |
| gg_imgname | Checks file names for ggsave |
| gn_rollup | Rolls up genes |
| go_sets_hs | Entrez IDs of human gene-ontology annotations. |
| go_sets_mm | Entrez IDs of mouse gene-ontology annotations. |
| go_sets_rn | Entrez IDs of rat gene-ontology annotations. |
| greedysetcover | Greedy set cover. |
| groupMZPepZ | Group Mzion peptides by charge states |
| groupMZPSM0 | Group PSMs |
| groupMZPSM1 | Group PSMs |
| Grubbs_outliers | Outlier removals with Grubbs's method |
| grubbs_test | Outlier removals with Grubbs' method |
| gspa_colAnnot | Sets up the column annotation in heat maps |
| gspaHM | Plots distance heat map of GSPA |
| gspaMap | Volcano plots of protein 'log2FC' under gene sets |
| gspa_summary_limma | GSPA pVal calculations using limma |
| gspa_summary_mean | gspa pVal calculations using geomean |
| gspaTest | Perform GSPA tests |
| gsvaTest | Perform GSVA tests |
| gsVolcano | Volcano plots of protein 'log2FC' under given gene sets |
| hadd_psm_apexes | Helper of adding PSM apexes |
| hdeduce_mod_indexes | Helper of deduce_mod_indexes. |
| hfind_fit_nms | Helper of find_fit_nms. |
| hfind_shared_prots | Helper of find_shared_prots. |
| hparse_fasta | Helper of parse_fasta by accession type. |
| hpeptideMBR | Helper of peptideMBR |
| hsub_by_bestz | Helper for subsetting PSMs by the best charge state under a... |
| hsubColnames | Helper of newColnames. |
| identical_dots | Compares dot-dot-dot between prior and current |
| impPepNA | Imputes NA values in a peptide table |
| imputeNA | Imputation of NA values |
| info_anal | Function factories for informatic analysis |
| ins_cols_after | Re-order columns in a data frame |
| is_all_nan | Finds all-NaN column(s) |
| is_trivial_col | Finds a trivial column |
| is_trivial_dbl | Finds a trivial vector |
| join_mgfs | Joins MGF data to MSGF outputs. |
| keep_psm_bestint | Keep the highest intensity PSM |
| kegg_sets_hs | Entrez IDs of human KEGG annotations. |
| kegg_sets_mm | Entrez IDs of mouse KEGG annotations. |
| kegg_sets_rn | Entrez IDs of rat KEGG annotations. |
| kinase_lookup | Lookups of human or mouse kinases. |
| kinsub_hs | Kinase (in gene name) and the the entrez IDs of substrates |
| kinsub_mm | Kinase (in gene name) and the the entrez IDs of substrates |
| kinsub_rn | Kinase (in gene name) and the the entrez IDs of substrates |
| KinSubTest | Analysis of kinase-substrate interactions |
| labEffPSM | TMT labeling efficiency |
| lgl_cleanup | Updates data groups of 'log2_R_' and 'I_' etc. by logical... |
| list_to_dataframe | Lists to a data frame |
| lm_gspa | significance tests of pVals between the up and the down... |
| lm_summary | Model summary |
| load_craps | Loads cRAPs |
| load_dbs | Loads species-specific Databases |
| load_expts | Loads TMT or LFQ experiments |
| load_fasta | Loads fasta |
| load_ls_group | Loads label_scheme or label_scheme_group. |
| load_prior | Loads prior Peptide.txt |
| load_psmC | Loads psmC.txt |
| load_stringdbs | Loads species-specific databases of STRING |
| locate_outliers | Locates the positions of outliers |
| make_cls | Make GSEA cls |
| make_frac_smry | Makes new frac_smry.xlsx. |
| make_gct | Make GSEA gct |
| makeLFQXYTS | Prepare the XYTS matrices for LFQ |
| make_mascot_intensities | Defines the intensity columns of Mascot outputs. |
| make_mascot_ratios | Defines the ratio columns of Mascot outputs. |
| make_mq_meta | Processes MaxQuant mqpar.xml |
| make_mq_meta2 | Processes MaxQuant mqpar.xml |
| map_essential | Helper for mapping between gene sets and essential gene sets |
| map_peps_prots | Helper: maps peptides to possible proteins |
| map_to_entrez | Map UniProt or Refseq accessions to Entrez IDs |
| map_to_entrez_os_name | Map uniprot or refseq to entrez (not currently used) |
| mart_hs | BioMart-Ensembl databases for human proteins. |
| mart_mm | BioMart-Ensembl for mouse proteins. |
| mart_rn | BioMart-Ensembl for rat proteins. |
| mascot_refseq2uniprot | Helper function |
| match_call_arg | Matches the arg to anal_prnGSPA |
| match_fmls | Matches formulas to those in calls to pepSig or prnSig |
| match_gset_nms | Matches gset_nms to prnGSPA. |
| match_logi_gv | A match to a global logical variable |
| match_pepSig_scale_log2r | Matches scale_log2r |
| match_prnSig_scale_log2r | Matches scale_log2r |
| maxquant_refseq2uniprot | Helper function |
| mcPSM | Median-centering normalization of PSM data |
| med_summarise_keys | Summary of peptide keys by mean or geomean |
| mergePep | Merge peptide table(s) into one |
| mfixBrukerMGF | Batch-fixing of Bruker MGF files. |
| mmbr_psms | Helper of smbr_psms. |
| model_onechannel | Factorial model formula for interaction terms. All factors... |
| mprocBrukerMGF | Batch-reprocessing of Bruker MGF files. |
| mq_mods | A list of MaxQuant modifications. |
| msubsetBrukerMGF | Parallel subsetBrukerMGF |
| my_complete_cases | Complete cases among sample IDs in label_scheme_sub, not... |
| my_custom_cor | Custom correlation plots |
| my_dist | A wrapper of dist with the handling of partial argument... |
| my_geomean | Geometric mean |
| my_padj | Adjusted pVal |
| my_pheatmap | A wrapper of pheatmap |
| my_sum_n | Sums top-n. |
| my_tolower | To lower cases |
| my_union | The union of named list |
| my_upper | To upper cases |
| my_which_max | Finds the x at max density. |
| na_genes_by_acc | Helper of parse_fasta. |
| names_pos-set | Prefix form of colnames(x)[c(2, 5, ...)] for use in pipes |
| na_single_lfq | Trivializes data rows with single LFQ intensity |
| na_species_by_org | Helper of parse_fasta. |
| na_zeroIntensity | Replaces zero intensity with NA |
| newColnames | Make new column names |
| n_LCMS | Finds the maximum number of LCMS injections under the same... |
| nmix_params | Helper of fitKernelDensity. |
| normMulGau | Data normalization |
| normPep | Combines peptide reports across multiple experiments. |
| normPSM | Standardization of PSM |
| normSD | Data normalization |
| not_all_NA | Finds not-all-NA column(s) |
| not_all_nan | Finds non-all-NaN column(s) |
| not_all_zero | Finds not-all-zero column(s) |
| not_allzero_rows | Finds all zero rows |
| n_TMT_sets | Finds the number of multiplex TMT experiments |
| ok_existing_params | Checks the suitability of existing param files for MGKernel |
| ok_file_ncomp | Compares to prior n_comp value. |
| ok_min_size | checks the size of a gene set |
| order_mascot_psm_cols | Orders Mascot PSM columns |
| order_psm_cols | Orders PSM columns. |
| pad_grp_samples | Pads sample groups. |
| pad_mascot_channels | Pads Mascot TMT channels to the highest plex |
| pad_mascot_fields | Pads Mascot PSM exports |
| pad_mf_channels | Pads MSFragger TMT channels to the highest plex. |
| pad_mq_channels | Pads MaxQuant TMT channels to the highest plex. |
| pad_psm_fields | Pads PSM exports. |
| pad_sm_channels | Pads Spectrum Mill TMT channels to the highest plex |
| pad_tmt_channels | Pads TMT channels to the highest multiplex. |
| parse_acc | Determines the protein accession type from PSM tables |
| parse_col_select | Parses 'col_select'. |
| parse_fasta | Parses FASTA for accession lookups |
| parse_filename | Parses file name. |
| p_dixon | Outlier removals with Dixon's method |
| Pep2Prn | Interim protein data |
| pep_mf_lfq | Handling of MSFragger peptide table |
| pep_mq_lfq | Handling of MaxQuant peptide.txt |
| peptideMBR | MBR of peptides |
| pep_to_prn | Helper of Pep2Prn |
| p_grubbs | Outlier removals with Grubbs' method |
| plotCorr | Correlation plots |
| plot_corr_sub | Make correlation plots |
| plotEucDist | Plots EucDist |
| plotHisto | Plots histograms |
| plotHM | Makes heat maps |
| plotLDA | Plots LDA |
| plotMDS | Plots MDS |
| plot_metaNMF | Heat maps of metagenes from NMF |
| plotNMFCoef | Plots coef results from NMF analysis |
| plotNMFCon | Plots consensus results from NMF analysis |
| plotNMFmeta | Plots coef results from NMF analysis |
| plotPCA | Plots PCA |
| plot_pepNMFCon | NMF plots |
| plot_prnTrend | Visualization of trend results |
| plotTrend | Plots trends |
| plot_venn | Plots Venn. |
| plotVolcano | Volcano plots |
| pre_mq_meta | Updates MaxQuant experimentalDesignTemplate.txt |
| prepDM | Prepares data for analysis |
| prepFml | Prepare formulas |
| prep_folded_tdata | Prepares folded, transposed data |
| prep_fraction_scheme | Loads the information of analyte prefractionation |
| prepGO | Download and prepare gene ontology |
| prep_gspa | Helper of GSPA |
| prep_label_scheme | Processes the metadata of TMT experiments |
| prepMSig | Preparation of Molecular Signatures |
| prep_range | Standardizes range values. |
| prepString | Downloads and prepares STRING databases |
| prn_annot_crap | Lookups of cRAP proteins. |
| prnCorr_logFC | Correlation plots |
| prnEucDist | Distance plots |
| prnGSEA | Protein GSEA |
| prnGSPA | GSPA of peptide data |
| prnGSPAHM | Heat map visualization of GSPA results |
| prnGSVA | GSVA of protein data |
| prnHist | Histogram visualization |
| prnHM | Visualization of heat maps |
| prnLDA | LDA plots |
| prnMDS | MDS plots |
| prnPCA | PCA plots |
| prnSig | Significance tests of peptide/protein log2FC |
| prnVol | Volcano plots |
| procBrukerMGF | Reprocesses of Bruker MGF files. |
| procBrukerMGF_v1 | Reprocesses of Bruker MGF files. |
| proc_gaf | Helper to save 'gaf' without header |
| proc_gmt | Helper to save 'gmt' |
| procMSGFmods | Processes MSGF modifications. |
| proc_obo | Helper to save 'obo' without header |
| procPSMs | Processes PSMs. |
| procTMT0 | Helper in reading TMTzero |
| proteo_hm | Makes heat maps |
| proteoQ | proteoQ: A package for processing mass spectrometry data. |
| PSM2Pep | Interim peptide tables |
| psm_mcleanup | Parallel PSM cleanup |
| psm_mpurge | Helper of purgePSM |
| psm_msplit | Splits of PSM tables |
| psm_to_pep | Helper of PSM2Pep |
| purge_by_cv | Filters data groups by a CV cut-off |
| purge_by_n | Filters data groups by a minimal number of observations... |
| purge_by_qt | Filters data groups by quantiles of CV |
| purgePep | Purges peptide data |
| purgePSM | Purges PSM data |
| pval_complete_cases | Helper of comeplet cases. |
| q_dixon | Distribution function |
| q_grubbs | Distribution function |
| q_table | Distribution table |
| ratio_toCtrl | Calculate the log2-ratio to the control group of samples |
| read_fasta | Reads a file in fasta format |
| read_metadata | Reads the metadata of expt_smry or frac_smry. |
| recheck_tmt_channels | Rechecks the completeness of TMT_Channel. |
| recur_flatten | Flattens lists recursively |
| refseq_entrez_hs | Lookups among RefSeq accessions, Entrez IDs and gene names... |
| refseq_entrez_mm | Lookups among RefSeq accessions, Entrez IDs and gene names... |
| refseq_entrez_rn | Lookups among RefSeq accessions, Entrez IDs and gene names... |
| reload_expts | Reloads the "expt_smry.xlsx" and "frac_smry.xlsx" |
| reloc_col | Relocates column "m/z" to be immediately before column... |
| reloc_col_after | Relocates column "to_move" immediately after column... |
| reloc_col_after_first | Relocates column "to_move" immediately after the first... |
| reloc_col_after_last | Relocates column "to_move" immediately after the last column. |
| reloc_col_before | Relocates column "to_move" immediately before anchor column... |
| reloc_col_before_first | Relocates column "to_move" immediately before the first... |
| reloc_col_before_last | Relocates column "to_move" immediately before the last... |
| reorderCols | Re-order columns in a data frame |
| reorderCols2 | Re-order columns in a data frame |
| reorder_files | Re-order file names |
| replace_by_rowone | Replaces values by the first row. |
| replace_cols_at | Replaces columns in the original PSM table. |
| replace_empty_with_na | Replaces 'Empty' 'Sample_ID"s with NA. |
| replace_na_genes | Replaces NA genes (not currently used) |
| replace_na_with_empty | Replaces NA sample IDs with Empty.1 etc. |
| replace_NorZ_names | Replaces column names to get Sample_ID(s). |
| replace_trivial_with_na | Replaces a trivial vector with NA values. |
| rep_ls_groups | Replicates new label_scheme with new Sample_IDs by group_ids. |
| rm_2RToutliers | Remove retention-time outliers between two |
| rm_apexrt_outliers | Remove PSM retention outliers |
| rm_cols_mqpsm | Removes columns from PSM table |
| rm_fully_empty_tmt_sets | Removes fully empty TMT sets. |
| rm_nRToutliers | Remove retention-time outliers for more than two values |
| rmPSMHeaders | Removes PSM headers |
| rm_psm_spikes | Remove PSM spikes by a group of 'pep_seq_modz' |
| rm_pval_whitespace | Checks file names for ggsave |
| rm_RToutliers | Cross-file removals of retention outliers |
| rm_sglval_cols | Removes single-value columns |
| Rosner_outliers | Outlier removals with Rosner's method |
| round_msfmod_decimals | For MSFragger |
| rowVars | Row Variance |
| rptr_violin | Violin plots of reporter-ion intensity per TMT_Set and... |
| save_call | Saves the arguments in a function call |
| scoreEucDist | Scores Euclidean distance |
| scoreLDA | Scores LDA |
| scoreMDS | Scores MDS |
| scorePCA | Scores PCA |
| sd_violin | Violin plots of CV per TMT_Set and LCMS_injection |
| sep_mbrfiles | Separate MBR file names by samples |
| set_cutpoints | Generates cut points. |
| set_cutpoints2 | A wrapper of 'set_cutpoint'. |
| set_dat_dir | Sets global 'dat_dir' |
| set_db_outname | Helper to set the output file name for a data base |
| set_ggsave_dots | Sets dot-dot-dot for ggsave. |
| setHMColor | Customizes the colors in column annotation |
| setHMlims | Sets the upper and the lower limits in the range of heat maps |
| set_mascot_colnms | Sets names for Mascot ratio and intensity columns. |
| sigTest | Significance tests |
| simple_label_scheme | Simplifies label schemes from 'label_scheme_full' |
| simulUniprotPSM | Generate simulated UniProt results from RefSeq PSM data |
| smbr_psms | Single MBR. |
| sort_tmt_lcms | Sorts by the indexes of TMT_Set and LCMS_Injection |
| spline_coefs | calculates the median-centered x's positions by spline points |
| splitPSM_ma | Splits PSM tables |
| splitPSM_mf | Splits MSFragger PSM tables |
| splitPSM_mq | Splits PSM tables |
| splitPSM_mz | Splits PSM tables from matchMS. |
| sp_lookup | Species lookup |
| sp_lookup_go | Helper to look up GO species |
| sp_lookup_Ul | Species lookup UpperLower (Ul) |
| spreadPepNums | Spreads peptide numbers. |
| standPep | Standardize peptide results |
| standPrn | Standardize protein results |
| stringTest | String analysis |
| sub_by_bestz | Subset PSMs by the best charge state under a 'pep_seq_mod' |
| subsetBrukerMGF | Subsets Bruker's MGF data |
| subset_fasta | Subsets fasta by accession type |
| subset_keepattr | Subsets elements with attributes kept. |
| subset_volcano_df | Sets data for volcano plots. |
| sumdnorm | Data normalization |
| summ_venn | Venn counts. |
| syn_empty_channels | Synchronizes Sample_ID(s) for Empty samples. |
| taxid_lookup | Taxonomy lookup |
| taxid_lookup_rev | Reversed taxonomy lookup |
| TMT_levels | Finds the factor levels of TMT labels |
| TMT_plex | Finds the multiplexity of TMT labels |
| TMT_plex2 | Finds the multiplexity of TMT labels from previously made... |
| TMT_top_n | Average top_n |
| tmt_wtmean | Calculates weighted mean |
| to_complete_cases | Forces 'complete_cases = TRUE' at 'impute_na = FALSE' |
| to_csv_ | Converts a data frame column to a csv vector |
| to_linfc | Converts log2FC to linear fold changes |
| triv_optcols_at_empty | Trivializes optional columns for Empty samples. |
| Uni2Entrez | Map UniProt accessions to Entrez IDs |
| uniprot_entrez_hs | Lookups between UniProt accessions and Entrez IDs for human... |
| uniprot_entrez_mm | Lookups between UniProt accessions and Entrez IDs for mouse... |
| uniprot_entrez_rn | Lookups between UniProt accessions and Entrez IDs for rat... |
| uniprot_species | A list of UniProt taxon IDs and Species names. |
| update_frac_smry | Updates pre-existed frac_smry.xlsx. |
| update_nodes | Helper of make_mq_meta2 |
| use_mf_peptable | Check the single presence of MSFragger peptide table |
| use_mf_prottable | Check the single presence of MSFragger... |
| use_mq_peptable | Check the single presence of MaxQuant peptides[...].txt. |
| use_mq_prottable | Check the single presence of MaxQuant... |
| vararg_secmsg | Helper for finding input 'df'. |
| write_excel_wb | Wrapper of writing Excel |
| write_fasta | Writes fasta |
| write_metadata | Writes the metadata of label_scheme or fraction_scheme. |
