API for qzhang503/proteoQ
Processing and Informatic Analysis of Mass Spectrometrirc Data
| Global functions | |
|---|---|
| .onAttach | Source code |
| Dixon_outliers | Man page Source code |
| Grubbs_outliers | Man page Source code |
| KinSubTest | Man page |
| PSM2Pep | Man page |
| Pep2Prn | Man page |
| Ref2Entrez | Man page |
| Rosner_outliers | Man page Source code |
| TMT_levels | Man page |
| TMT_plex | Man page |
| TMT_plex2 | Man page |
| TMT_top_n | Man page |
| Uni2Entrez | Man page |
| aa_residues | Man page |
| addApexRTs | Man page |
| addApexes | Man page Source code |
| addMBRpeps | Man page |
| add_col_rawfile | Man page |
| add_cols_at | Man page |
| add_custom_entrez | Man page |
| add_empai | Man page |
| add_entrez | Man page |
| add_entry_ids | Man page |
| add_fasta_attrs | Man page |
| add_mascot_pepseqmod | Man page |
| add_mascot_raw | Man page |
| add_maxquant_pepseqmod | Man page |
| add_mean_dev | Man page |
| add_mod_conf | Man page |
| add_msfragger_pepseqmod | Man page |
| add_msgf_pepseqmod | Man page |
| add_n_pepexpz | Man page |
| add_pep_n_apexes | Man page |
| add_pep_retsd | Man page |
| add_pepseqmod | Man page |
| add_prot_desc | Man page |
| add_prot_icover | Man page |
| add_quality_cols | Man page |
| add_refseq_gene | Man page |
| add_scan_id | Man page |
| add_shared_genes | Man page |
| add_shared_prot_accs_mf | Man page |
| add_shared_sm_genes | Man page |
| add_sm_pepseqmod | Man page |
| add_spec_counts | Man page |
| aggrLFQs | Man page |
| aggrNumLCMS | Man page |
| aggrNums | Man page |
| aggrTopn | Man page |
| alignPSMApexs | Man page |
| analNMF | Man page Source code |
| analTrend | Man page |
| anal_KinSub | Man page |
| anal_pepNMF | Man page |
| anal_prnNMF | Man page |
| anal_prnString | Man page |
| anal_prnTrend | Man page |
| annotKin | Man page |
| annotPSM | Man page |
| annotPeppos | Man page |
| annotPrn | Man page |
| annot_KinSub | Man page Source code |
| annot_from_to | Man page |
| annot_stringdb | Man page Source code |
| arrangers_in_call | Man page |
| assign_duppeps | Man page |
| batchPSMheader | Man page |
| byfile_gspahm | Man page |
| byfile_plotVolcano | Man page |
| byfml_gspahm | Man page |
| byfml_volcano | Man page |
| c2_msig_hs | Man page |
| c2_msig_mm | Man page |
| c2_msig_rn | Man page |
| calcLFQPepInts | Man page |
| calcLFQPepNums | Man page |
| calcLFQPeptide | Man page |
| calcLFQprnnums | Man page |
| calcSD_Splex | Man page |
| calcTMTLFQPeptide | Man page |
| calcTMTLabs | Man page |
| calc_avgpep | Man page |
| calc_cover | Man page |
| calc_lfq_log2r | Man page |
| calc_mat_log2s_to_refs | Man page |
| calc_mat_sds | Man page |
| calc_mq_log2r | Man page |
| calc_pep_retsd | Man page |
| calc_sd_fcts | Man page |
| calc_sd_fcts_psm | Man page |
| calc_tmt_prnnums | Man page |
| calc_vec_log2s_to_refs | Man page |
| calibPSMApexs2 | Man page |
| center_df | Man page |
| channelInfo | Man page |
| check_aes_length | Man page |
| check_channel_prefix | Man page |
| check_depreciated_args | Man page |
| check_dots | Man page |
| check_dup_unimods | Man page |
| check_dups_at_lcms_and_sid | Man page |
| check_empty_rows | Man page |
| check_exptfrac_raws | Man page |
| check_formalArgs | Man page |
| check_formalArgs2 | Man page |
| check_frac_multipsms | Man page |
| check_ggplot_aes | Man page |
| check_gset_nms | Man page |
| check_lfq_exptraws | Man page |
| check_metadata_integers | Man page |
| check_mq_df | Man page |
| check_optional_cols | Man page |
| check_raws | Man page |
| check_required_cols | Man page |
| check_tmt126_row | Man page |
| check_tmt_chans_vs_levs | Man page |
| check_tmt_emptyids | Man page |
| check_tmt_mixplexes | Man page |
| check_tmt_nc | Man page |
| check_tmt_plex | Man page |
| check_tmt_rawfiles | Man page |
| check_tmt_ref | Man page |
| check_tmt_sampleids | Man page |
| check_unnamed_cols | Man page |
| checkdots_analTrend | Man page Source code |
| checkmzLFQRT | Man page |
| cleanPSMYTS | Man page |
| cleanRTChim | Man page |
| cleanupPSM | Man page |
| cluego | Man page |
| cmbn_meta | Man page |
| colAnnot | Man page |
| collapseSTY | Man page |
| collapse_psm_charges | Man page |
| combine_lfq123 | Man page |
| compile_hdr_mods | Man page |
| concat_fml_dots | Man page |
| contain_chars_in | Man page |
| contain_str | Man page |
| cos_sim | Man page |
| countSpecs | Man page |
| count_pepmiss | Man page |
| count_phosphopeps | Man page |
| create_db_path | Man page |
| create_os_lookup | Man page |
| dblTrim | Man page |
| deduce_mod_indexes | Man page |
| dixon_test | Man page |
| dl_msig | Man page |
| end_with_str | Man page |
| ends_with_chars_in | Man page |
| env_where | Man page |
| extract_mbry | Man page |
| extract_mq_ints | Man page |
| extract_psm_raws | Man page |
| extract_raws | Man page Source code |
| fillMBRnaRTs | Man page |
| fillMFprnnums | Man page |
| fillMQprnnums | Man page |
| filterData | Man page |
| filters_in_call | Man page |
| find_NorZ | Man page |
| find_abbr_species | Man page |
| find_best_lfqvec | Man page |
| find_delim | Man page |
| find_fit_nms | Man page Source code |
| find_fn_bases | Man page |
| find_fn_exts | Man page |
| find_human_orthologs | Man page |
| find_int_cols | Man page |
| find_mascot_plex | Man page |
| find_mascot_psmraws | Man page Source code |
| find_mascot_tmtplex | Man page |
| find_mascot_vmods | Man page |
| find_mbr_ms1files | Man page |
| find_mf_psmraws | Man page |
| find_mod_indexesQ | Man page |
| find_mq_psmraws | Man page |
| find_ms1filepath | Man page |
| find_n_comp | Man page |
| find_padding_pos | Man page |
| find_path_ms1 | Man page |
| find_pep_pos | Man page |
| find_pq_psmraws | Man page |
| find_preceding_colnm | Man page |
| find_pri_df | Man page |
| find_prot_family_rows | Man page |
| find_psmQ_files | Man page |
| find_ratio_cols | Man page |
| find_search_engine | Man page |
| find_sec_df | Man page |
| find_shared_prots | Man page |
| find_sm_psmraws | Man page |
| find_species_centers | Man page |
| find_species_centers2 | Man page |
| fitKernelDensity | Man page |
| fitMS1RT | Man page |
| fixBrukerMGF | Man page |
| fml2mass | Man page |
| fml_gsea | Man page |
| fml_gspa | Man page |
| fmt_num_cols | Man page |
| fullVolcano | Man page |
| geom_lower_text | Man page Source code |
| geom_table | Man page |
| get_col_types | Man page |
| get_full_entrez | Man page |
| get_gl_dat_dir | Man page Source code |
| gg_imgname | Man page |
| gn_rollup | Man page |
| go_sets_hs | Man page |
| go_sets_mm | Man page |
| go_sets_rn | Man page |
| greedysetcover | Man page |
| groupMZPSM0 | Man page |
| groupMZPSM1 | Man page |
| groupMZPepZ | Man page |
| groupMZPepZ2 | Man page |
| grubbs_test | Man page |
| gsVolcano | Man page |
| gspaHM | Man page |
| gspaMap | Man page |
| gspaTest | Man page |
| gspa_colAnnot | Man page |
| gspa_summary_limma | Man page |
| gspa_summary_mean | Man page |
| gsvaTest | Man page |
| haddApexRTs_allsets | Man page |
| haddApexRTs_oneset | Man page |
| hdeduce_mod_indexes | Man page |
| hfind_fit_nms | Man page |
| hfind_shared_prots | Man page |
| hparse_fasta | Man page |
| hpepLFQ | Man page |
| hrm_lowIntPSMs | Man page |
| hsubColnames | Man page |
| identical_dots | Man page |
| impPepNA | Man page |
| impRefNA | Man page |
| imputeNA | Man page |
| info_anal | Man page |
| ins_cols_after | Man page |
| is_all_nan | Man page |
| is_trivial_col | Man page |
| is_trivial_dbl | Man page |
| join_mgfs | Man page |
| keep_psm_bestint | Man page |
| kegg_sets_hs | Man page |
| kegg_sets_mm | Man page |
| kegg_sets_rn | Man page |
| kinase_lookup | Man page |
| kinsub_hs | Man page |
| kinsub_mm | Man page |
| kinsub_rn | Man page |
| labEffPSM | Man page Source code |
| lgl_cleanup | Man page |
| list_to_dataframe | Man page |
| lm_gspa | Man page |
| lm_summary | Man page |
| load_craps | Man page |
| load_dbs | Man page |
| load_expts | Man page |
| load_fasta | Man page |
| load_ls_group | Man page |
| load_prior | Man page |
| load_psmC | Man page |
| load_stringdbs | Man page |
| locate_outliers | Man page |
| makeLFQSpecies | Man page |
| makeLFQXYTS | Man page |
| make_cls | Man page Source code |
| make_frac_smry | Man page |
| make_gct | Man page Source code |
| make_mascot_intensities | Man page |
| make_mascot_ratios | Man page |
| make_mq_meta | Man page |
| make_mq_meta2 | Man page |
| map_essential | Man page |
| map_peps_prots | Man page |
| map_to_entrez | Man page |
| map_to_entrez_os_name | Man page |
| mart_hs | Man page |
| mart_mm | Man page |
| mart_rn | Man page |
| mascot_refseq2uniprot | Man page Source code |
| match_call_arg | Man page |
| match_fmls | Man page |
| match_gset_nms | Man page |
| match_logi_gv | Man page |
| match_pepSig_scale_log2r | Man page |
| match_prnSig_scale_log2r | Man page |
| maxquant_refseq2uniprot | Man page Source code |
| mcPSM | Man page |
| med_summarise_keys | Man page |
| mergePep | Man page |
| mergeSTY | Man page |
| mfixBrukerMGF | Man page |
| model_onechannel | Man page |
| mpepLFQ | Man page |
| mprocBrukerMGF | Man page |
| mq_mods | Man page |
| msubsetBrukerMGF | Man page |
| my_complete_cases | Man page |
| my_custom_cor | Man page |
| my_dist | Man page |
| my_geomean | Man page |
| my_padj | Man page |
| my_pheatmap | Man page Source code |
| my_split1 | Man page |
| my_split2 | Man page |
| my_sum_n | Man page |
| my_tolower | Man page |
| my_toupper | Man page |
| my_union | Man page |
| my_which_max | Man page |
| n_LCMS | Man page |
| n_TMT_sets | Man page |
| na_genes_by_acc | Man page |
| na_single_lfq | Man page |
| na_species_by_org | Man page |
| na_zeroIntensity | Man page |
| names_pos<- | Man page |
| newColnames | Man page Source code |
| nmix_params | Man page |
| normMulGau | Man page |
| normPSM | Man page |
| normPep | Man page |
| normSD | Man page |
| not_all_NA | Man page |
| not_all_nan | Man page |
| not_all_zero | Man page |
| not_allzero_rows | Man page |
| not_contain_chars_in | Man page |
| not_contain_str | Man page |
| ok_existing_params | Man page |
| ok_file_ncomp | Man page |
| ok_min_size | Man page |
| order_mascot_psm_cols | Man page |
| order_psm_cols | Man page |
| p_dixon | Man page |
| p_grubbs | Man page |
| pad_grp_samples | Man page |
| pad_mascot_channels | Man page |
| pad_mascot_fields | Man page |
| pad_mf_channels | Man page |
| pad_mq_channels | Man page |
| pad_psm_fields | Man page |
| pad_sm_channels | Man page |
| pad_tmt_channels | Man page |
| parse_acc | Man page |
| parse_col_select | Man page |
| parse_fasta | Man page |
| parse_filename | Man page |
| pepCorr_logFC | Man page |
| pepCorr_logInt | Man page |
| pepEucDist | Man page |
| pepGSPA | Man page |
| pepHM | Man page |
| pepHist | Man page |
| pepImp | Man page |
| pepLDA | Man page |
| pepLFQ | Man page |
| pepLFQ2 | Man page |
| pepMDS | Man page |
| pepPCA | Man page |
| pepSig | Man page |
| pepVol | Man page |
| pep_mf_lfq | Man page |
| pep_mq_lfq | Man page |
| pep_to_prn | Man page |
| plotCorr | Man page |
| plotEucDist | Man page |
| plotHM | Man page |
| plotHisto | Man page |
| plotLDA | Man page |
| plotMDS | Man page |
| plotNMFCoef | Man page |
| plotNMFCon | Man page |
| plotNMFmeta | Man page |
| plotPCA | Man page |
| plotTrend | Man page |
| plotVolcano | Man page Source code |
| plot_corr_sub | Man page |
| plot_metaNMF | Man page |
| plot_pepNMFCoef | Man page |
| plot_pepNMFCon | Man page |
| plot_prnNMFCoef | Man page |
| plot_prnNMFCon | Man page |
| plot_prnTrend | Man page |
| plot_venn | Man page |
| point_in_polygon | Man page |
| postMZpepLFQ | Man page |
| preMZpepLFQ | Man page |
| pre_mq_meta | Man page |
| prepDM | Man page Source code |
| prepFml | Man page |
| prepGO | Man page |
| prepMSig | Man page |
| prepString | Man page |
| prep_folded_tdata | Man page |
| prep_fraction_scheme | Man page |
| prep_gspa | Man page |
| prep_label_scheme | Man page Source code |
| prep_range | Man page |
| prnCorr_logFC | Man page |
| prnCorr_logInt | Man page |
| prnEucDist | Man page |
| prnGSEA | Man page |
| prnGSPA | Man page |
| prnGSPAHM | Man page |
| prnGSVA | Man page |
| prnHM | Man page |
| prnHist | Man page |
| prnImp | Man page |
| prnLDA | Man page |
| prnMDS | Man page |
| prnPCA | Man page |
| prnSig | Man page |
| prnVol | Man page |
| prn_annot_crap | Man page |
| procBrukerMGF | Man page |
| procBrukerMGF_v1 | Man page |
| procMSGFmods | Man page |
| procPSMs | Man page |
| procTMT0 | Man page |
| proc_gaf | Man page |
| proc_gmt | Man page |
| proc_obo | Man page Source code |
| proteoQ | Man page |
| proteoQ-package | Man page |
| proteo_hm | Man page Source code |
| psm_mcleanup | Man page |
| psm_mpurge | Man page |
| psm_msplit | Man page |
| psm_to_pep | Man page |
| purgePSM | Man page |
| purgePep | Man page |
| purge_by_cv | Man page |
| purge_by_n | Man page |
| purge_by_qt | Man page |
| pval_complete_cases | Man page |
| q_dixon | Man page |
| q_grubbs | Man page |
| q_table | Man page |
| ratio_toCtrl | Man page |
| read_fasta | Man page |
| read_metadata | Man page |
| recheck_tmt_channels | Man page |
| recur_flatten | Man page |
| reduce_lfq_rtstep | Man page |
| refseq_entrez_hs | Man page |
| refseq_entrez_mm | Man page |
| refseq_entrez_rn | Man page |
| reload_expts | Man page |
| reloc_col | Man page |
| reloc_col_after | Man page |
| reloc_col_after_first | Man page |
| reloc_col_after_last | Man page |
| reloc_col_before | Man page |
| reloc_col_before_first | Man page |
| reloc_col_before_last | Man page |
| reorderCols | Man page |
| reorderCols2 | Man page |
| reorder_files2 | Man page |
| rep_ls_groups | Man page |
| replace_NorZ_names | Man page |
| replace_by_rowone | Man page |
| replace_cols_at | Man page |
| replace_empty_with_na | Man page |
| replace_na_genes | Man page |
| replace_na_with_empty | Man page |
| replace_trivial_with_na | Man page |
| rmPSMHeaders | Man page |
| rm_2RToutliers | Man page |
| rm_RToutliers | Man page |
| rm_apexrt_outliers | Man page |
| rm_cols_mqpsm | Man page |
| rm_fully_empty_tmt_sets | Man page |
| rm_lowIntPSMs | Man page |
| rm_nRToutliers | Man page |
| rm_psm_spikes | Man page |
| rm_pval_whitespace | Man page |
| rm_sglval_cols | Man page |
| round_msfmod_decimals | Man page |
| rowVars | Man page |
| rows_are_all | Man page |
| rows_are_not_all | Man page |
| rptr_violin | Man page |
| saddMBR | Man page |
| save_call | Man page |
| scoreEucDist | Man page |
| scoreLDA | Man page |
| scoreMDS | Man page |
| scorePCA | Man page |
| sd_violin | Man page |
| sep_mbrfiles | Man page |
| setHMColor | Man page |
| setHMlims | Man page |
| set_cutpoints | Man page |
| set_cutpoints2 | Man page |
| set_dat_dir | Man page Source code |
| set_db_outname | Man page |
| set_ggsave_dots | Man page |
| set_mascot_colnms | Man page |
| sigTest | Man page |
| simple_label_scheme | Man page |
| simulUniprotPSM | Man page Source code |
| sort_tmt_lcms | Man page |
| sp_lookup | Man page |
| sp_lookup_Ul | Man page |
| sp_lookup_go | Man page |
| spline_coefs | Man page |
| splitPSM_ma | Man page |
| splitPSM_mf | Man page |
| splitPSM_mq | Man page |
| splitPSM_mz | Man page |
| spreadPepNums | Man page |
| standPep | Man page |
| standPrn | Man page |
| start_with_chars_in | Man page |
| start_with_str | Man page |
| stringTest | Man page |
| subsetBrukerMGF | Man page |
| subset_fasta | Man page |
| subset_keepattr | Man page |
| subset_volcano_df | Man page |
| sumdnorm | Man page |
| summ_venn | Man page |
| syn_empty_channels | Man page |
| taxid_lookup | Man page |
| taxid_lookup_rev | Man page |
| tmt_wtmean | Man page |
| to_complete_cases | Man page |
| to_csv_ | Man page |
| to_linfc | Man page |
| triv_optcols_at_empty | Man page |
| uniprot_entrez_hs | Man page |
| uniprot_entrez_mm | Man page |
| uniprot_entrez_rn | Man page |
| uniprot_species | Man page |
| updatePSMsd | Man page |
| update_frac_smry | Man page |
| update_nodes | Man page |
| use_mf_peptable | Man page |
| use_mf_prottable | Man page |
| use_mq_peptable | Man page |
| use_mq_prottable | Man page |
| vararg_secmsg | Man page |
| write_excel_wb | Man page |
| write_fasta | Man page |
| write_metadata | Man page |
