R/funs.R
In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data
# $cluego_api.R
# [1] "cluego"
#
# $corrplots.R
# [1] "plotCorr" "my_custom_cor" " percent_of_range" "plot_corr_sub" " my_fn"
# [6] " lm_with_cor" " panel_cor" " panel_hist" " panel_lm" " my_lower"
# [11] " my_lower_no_sm" " my_diag" "pepCorr_logFC" "pepCorr_logInt" "prnCorr_logFC"
# [16] "prnCorr_logInt"
#
# $datasets.R
# character(0)
#
# $dbs.R
# [1] "read_fasta" "write_fasta" "load_fasta" "calc_avgpep"
#
# $global.R
# [1] "set_dat_dir" "get_gl_dat_dir"
#
# $go.R
# [1] "create_db_path" "proc_obo" "proc_gaf" "annot_from_to" "get_full_entrez"
# [6] "find_human_orthologs" "sp_lookup_go" "find_abbr_species" "set_db_outname" "dl_msig"
# [11] "proc_gmt" "prepGO" "prepMSig" "map_to_entrez" "Uni2Entrez"
# [16] "Ref2Entrez" "map_to_entrez_os_name" "create_os_lookup" " convert_default_os"
#
# $gsea.R
# [1] "make_gct" "make_cls" "prnGSEA" "fml_gsea"
#
# $gspa.R
# [1] "pepGSPA" "prnGSPA" "gspaTest" "fml_gspa" "ok_min_size"
# [6] "gspa_summary_mean" "gspa_summary_limma" "lm_gspa" "prep_gspa" "map_essential"
# [11] "prnGSPAHM" "gspaHM" "byfml_gspahm" "byfile_gspahm" "gspa_colAnnot"
# [16] "greedysetcover"
#
# $gsva.R
# [1] "prnGSVA" "gsvaTest"
#
# $histo.R
# [1] "plotHisto" "pepHist" "prnHist"
#
# $hm.R
# [1] "my_pheatmap" "plotHM" "pepHM" "prnHM"
#
# $informatics.R
# [1] "info_anal" "find_pri_df" "find_sec_df" "vararg_secmsg"
#
# $kin.R
# [1] "annot_KinSub" "KinSubTest" "anal_KinSub"
#
# $lda.R
# [1] "plotLDA" "scoreLDA" "pepLDA" "prnLDA"
#
# $mds.R
# [1] "geom_lower_text" "plotMDS" "plotEucDist" "scoreMDS" "prep_folded_tdata" "scoreEucDist"
# [7] "pepMDS" "prnMDS" "pepEucDist" "prnEucDist"
#
# $metadata.R
# [1] "prep_label_scheme" "prep_fraction_scheme" "update_frac_smry" "make_frac_smry"
# [5] "check_frac_multipsms" "check_exptfrac_raws" "read_metadata" "write_metadata"
# [9] "check_unnamed_cols" "check_required_cols" "check_optional_cols" "check_empty_rows"
# [13] "check_tmt126_row" "check_tmt_nc" "check_tmt_plex" "check_channel_prefix"
# [17] "check_tmt_ref" "rm_fully_empty_tmt_sets" "replace_empty_with_na" "replace_na_with_empty"
# [21] "check_metadata_integers" "syn_empty_channels" "triv_optcols_at_empty" "recheck_tmt_channels"
# [25] "check_tmt_rawfiles" "check_tmt_sampleids" "check_tmt_emptyids" "check_tmt_chans_vs_levs"
# [29] "check_tmt_mixplexes" "check_dups_at_lcms_and_sid" "check_lfq_exptraws" "load_dbs"
# [33] "load_expts" "reload_expts" "channelInfo" "n_TMT_sets"
# [37] "n_LCMS" "TMT_plex" "TMT_plex2" "TMT_levels"
# [41] "simple_label_scheme" "find_mascot_tmtplex"
#
# $nmf.R
# [1] "analNMF" "plotNMFCon" "plotNMFCoef" "plotNMFmeta" "anal_pepNMF" "anal_prnNMF"
# [7] "plot_pepNMFCon" "plot_prnNMFCon" "plot_pepNMFCoef" "plot_prnNMFCoef" "plot_metaNMF"
#
# $normalization.R
# [1] "find_fit_nms" "hfind_fit_nms" "calc_sd_fcts" "center_df" "add_mean_dev" "find_n_comp"
# [7] "my_which_max" "ok_file_ncomp" "spline_coefs" "normMulGau" "dblTrim" "sumdnorm"
# [13] " wt_dnorm" "normSD" "fitKernelDensity" "nmix_params"
#
# $outliers.R
# [1] "locate_outliers" "dixon_test" "q_dixon" "p_dixon" "q_table" "Dixon_outliers"
# [7] "Grubbs_outliers" "grubbs_test" "q_grubbs" " f" "p_grubbs" "Rosner_outliers"
#
# $pca.R
# [1] "plotPCA" "scorePCA" "pepPCA" "prnPCA"
#
# $peptable.R
# [1] "newColnames" "hsubColnames" "use_mq_peptable" "single_mq_prntable" "check_mq_df"
# [6] "extract_mq_ints" " calc_mq_log2r" "pep_mq_lfq" "pep_mq_lfq2" "calc_lfq_log2r"
# [11] "na_single_lfq" "calclfqPepNums" "calclfqPepInts" "spreadPepNums" "aggrNumLCMS"
# [16] "pad_grp_samples" "rep_ls_groups" "normPep_Mplex" "med_summarise_keys" "load_prior"
# [21] "fmt_num_cols" "mergePep" "standPep" "Pep2Prn" "map_peps_prots"
# [26] "find_prot_family_rows" "my_sum_n" "calc_lfq_prnnums" "calc_tmt_prnnums" "pep_to_prn"
# [31] "assign_duppeps" "replace_by_rowone"
#
# $prntable.R
# [1] "standPrn"
#
# $proteoQ.R
# character(0)
#
# $psmtable.R
# [1] "extract_raws"
# [2] "find_mascot_psmraws <-function(filelist = NULL, dat_dir = NULL)"
# [3] "find_mq_psmraws"
# [4] "find_sm_psmraws"
# [5] "find_mf_psmraws"
# [6] "find_pq_psmraws"
# [7] "extract_psm_raws"
# [8] "set_mascot_colnms"
# [9] "batchPSMheader"
# [10] "rmPSMHeaders"
# [11] "add_mod_conf"
# [12] "find_mascot_vmods"
# [13] "add_mascot_pepseqmod"
# [14] "add_empai"
# [15] "add_quality_cols"
# [16] "psm_msplit"
# [17] "find_shared_prots"
# [18] "hfind_shared_prots"
# [19] "add_shared_genes"
# [20] "add_shared_prot_accs_mf"
# [21] "add_shared_sm_genes"
# [22] "procPSMs"
# [23] "check_raws"
# [24] "splitPSM"
# [25] "find_mascot_plex"
# [26] "make_mascot_ratios"
# [27] "make_mascot_intensities"
# [28] "add_mascot_raw"
# [29] "pad_mascot_channels"
# [30] "pad_mascot_fields"
# [31] "psm_mcleanup"
# [32] "cleanupPSM"
# [33] "mcPSM"
# [34] "annotPSM"
# [35] "normPSM"
# [36] "rm_cols_mqpsm"
# [37] "calcPeptide"
# [38] "psm_to_pep"
# [39] "PSM2Pep"
# [40] "my_tolower"
# [41] "my_upper"
# [42] "add_maxquant_pepseqmod"
# [43] "add_msfragger_pepseqmod"
# [44] "add_cols_at"
# [45] "replace_cols_at"
# [46] "reloc_col"
# [47] "reloc_col_after"
# [48] "reloc_col_after_last"
# [49] "reloc_col_after_first"
# [50] "reloc_col_before"
# [51] "reloc_col_before_last"
# [52] "reloc_col_before_first"
# [53] "find_preceding_colnm"
# [54] "order_psm_cols"
# [55] "order_mascot_psm_cols"
# [56] "pad_mq_channels"
# [57] "splitPSM_mq"
# [58] "pad_sm_channels"
# [59] "add_sm_pepseqmod"
# [60] "splitPSM_sm"
# [61] "pad_mf_channels"
# [62] "splitPSM_mf"
# [63] "find_padding_pos"
# [64] "pad_tmt_channels"
# [65] "pad_psm_fields"
# [66] "add_pepseqmod"
# [67] "check_dup_unimods"
# [68] "splitPSM_pq"
# [69] "add_pep_retsd"
# [70] "calc_pep_retsd"
# [71] "add_n_pepexpz"
#
# $purge.R
# [1] "lgl_cleanup" "purge_by_cv" "purge_by_qt" "purge_by_n" "psm_mpurge" "purgePSM" "purgePep"
#
# $roadmap.R
# character(0)
#
# $sigtests.R
# [1] "rowVars" "filterData" "prepFml" "my_padj" "lm_summary" "model_onechannel"
# [7] "sigTest" "pepSig" "prnSig"
#
# $simulData.R
# [1] "simulUniprotPSM" "mascot_refseq2uniprot" "maxquant_refseq2uniprot"
#
# $specialty.R
# [1] "labEffPSM" "procTMT0" "calcTMTLabs" "proteo_hm"
#
# $string.R
# [1] "annot_stringdb" "stringTest" "anal_prnString" "prepString" "load_stringdbs"
#
# $trends.R
# [1] "checkdots_analTrend" "analTrend" "plotTrend" "anal_prnTrend" "plot_prnTrend"
#
# $utils.R
# [1] "prepDM" "find_NorZ" "replace_NorZ_names" "`names_pos<-`"
# [5] "reorder_files" "reorderCols" "reorderCols2" "ins_cols_after"
# [9] "sort_tmt_lcms" "na_zeroIntensity" "not_allzero_rows" "aggrNums"
# [13] "aggrTopn" "aggrLFQs" "tmt_wtmean" " my_trim"
# [17] " my_wtmean" "TMT_top_n" "not_all_zero" "not_all_NA"
# [21] "not_all_nan" "is_all_nan" "is_trivial_col" "is_trivial_dbl"
# [25] "replace_trivial_with_na" "colAnnot" "setHMColor" "setHMlims"
# [29] "ratio_toCtrl" "imputeNA" " my_mice" " handleNA"
# [33] "pepImp" "prnImp" "sp_lookup" "taxid_lookup"
# [37] "taxid_lookup_rev" "sp_lookup_Ul" "add_refseq_gene" "add_entrez"
# [41] "add_custom_entrez" "parse_acc" "parse_fasta" "hparse_fasta"
# [45] "na_genes_by_acc" "na_species_by_org" "add_fasta_attrs" "add_prot_desc"
# [49] "annotPrn" " na_fasta_name_by_prot_acc" " na_acc_type_to_other" "annotKin"
# [53] "save_call" "match_fmls" "match_call_arg" "match_gset_nms"
# [57] "#' foo" "match_logi_gv" "match_prnSig_scale_log2r" "match_pepSig_scale_log2r"
# [61] "replace_na_genes" "na_genes_by_acc" "find_pep_pos" "annotPeppos"
# [65] "subset_fasta" "add_prot_icover" "calc_cover" "to_linfc"
# [69] "rm_sglval_cols" "cmbn_meta" "gg_imgname" "rm_pval_whitespace"
# [73] "filters_in_call" "arrangers_in_call" "calc_sd_fcts_psm" "calcSD_Splex"
# [77] "sd_violin" "rptr_violin" "my_geomean" "count_phosphopeps"
# [81] "count_pepmiss" "contain_str" "contain_chars_in" "not_contain_str"
# [85] "not_contain_chars_in" "start_with_str" "end_with_str" "start_with_chars_in"
# [89] "ends_with_chars_in" "rows_are_all" "rows_are_not_all" "concat_fml_dots"
# [93] "gn_rollup" "identical_dots" "my_complete_cases" "my_union"
# [97] "find_fn_bases" "find_fn_exts" "check_dots" "check_depreciated_args"
# [101] "to_complete_cases" "check_gset_nms" "ok_existing_params" "env_where"
# [105] "set_cutpoints" "set_cutpoints2" "load_craps" "find_int_cols"
# [109] "find_ratio_cols" "make_mq_meta" "make_mq_meta2" " update_nodes"
# [113] "add_entry_ids" "check_formalArgs" "check_formalArgs2" "set_ggsave_dots"
# [117] "find_search_engine" "check_ggplot_aes" "prep_range" "find_delim"
# [121] "recur_flatten" "subset_keepattr" "list_to_dataframe" "find_psmQ_files"
# [125] "get_col_types" "write_excel_wb" "load_ls_group" "parse_col_select"
# [129] "parse_filename" "procBrukerMGF" "procBrukerMGF_v1" "mprocBrukerMGF"
# [133] "check_aes_length"
#
# $utils_proteom.R
# [1] "find_mod_indexesQ" "deduce_mod_indexes" "hdeduce_mod_indexes"
#
# $volcanos.R
# [1] "plotVolcano" "pval_complete_cases" "byfml_volcano" "byfile_plotVolcano" "subset_volcano_df"
# [6] "fullVolcano" "summ_venn" "plot_venn" "gsVolcano" "pepVol"
# [11] "prnVol" "gspaMap" "geom_table" "to_csv_"
#
# $wrappers.R
# [1] "my_dist" "cos_sim"
#
# $zzz.R
# [1] ".onAttach"
#
qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.
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# $cluego_api.R
# [1] "cluego"
#
# $corrplots.R
# [1] "plotCorr" "my_custom_cor" " percent_of_range" "plot_corr_sub" " my_fn"
# [6] " lm_with_cor" " panel_cor" " panel_hist" " panel_lm" " my_lower"
# [11] " my_lower_no_sm" " my_diag" "pepCorr_logFC" "pepCorr_logInt" "prnCorr_logFC"
# [16] "prnCorr_logInt"
#
# $datasets.R
# character(0)
#
# $dbs.R
# [1] "read_fasta" "write_fasta" "load_fasta" "calc_avgpep"
#
# $global.R
# [1] "set_dat_dir" "get_gl_dat_dir"
#
# $go.R
# [1] "create_db_path" "proc_obo" "proc_gaf" "annot_from_to" "get_full_entrez"
# [6] "find_human_orthologs" "sp_lookup_go" "find_abbr_species" "set_db_outname" "dl_msig"
# [11] "proc_gmt" "prepGO" "prepMSig" "map_to_entrez" "Uni2Entrez"
# [16] "Ref2Entrez" "map_to_entrez_os_name" "create_os_lookup" " convert_default_os"
#
# $gsea.R
# [1] "make_gct" "make_cls" "prnGSEA" "fml_gsea"
#
# $gspa.R
# [1] "pepGSPA" "prnGSPA" "gspaTest" "fml_gspa" "ok_min_size"
# [6] "gspa_summary_mean" "gspa_summary_limma" "lm_gspa" "prep_gspa" "map_essential"
# [11] "prnGSPAHM" "gspaHM" "byfml_gspahm" "byfile_gspahm" "gspa_colAnnot"
# [16] "greedysetcover"
#
# $gsva.R
# [1] "prnGSVA" "gsvaTest"
#
# $histo.R
# [1] "plotHisto" "pepHist" "prnHist"
#
# $hm.R
# [1] "my_pheatmap" "plotHM" "pepHM" "prnHM"
#
# $informatics.R
# [1] "info_anal" "find_pri_df" "find_sec_df" "vararg_secmsg"
#
# $kin.R
# [1] "annot_KinSub" "KinSubTest" "anal_KinSub"
#
# $lda.R
# [1] "plotLDA" "scoreLDA" "pepLDA" "prnLDA"
#
# $mds.R
# [1] "geom_lower_text" "plotMDS" "plotEucDist" "scoreMDS" "prep_folded_tdata" "scoreEucDist"
# [7] "pepMDS" "prnMDS" "pepEucDist" "prnEucDist"
#
# $metadata.R
# [1] "prep_label_scheme" "prep_fraction_scheme" "update_frac_smry" "make_frac_smry"
# [5] "check_frac_multipsms" "check_exptfrac_raws" "read_metadata" "write_metadata"
# [9] "check_unnamed_cols" "check_required_cols" "check_optional_cols" "check_empty_rows"
# [13] "check_tmt126_row" "check_tmt_nc" "check_tmt_plex" "check_channel_prefix"
# [17] "check_tmt_ref" "rm_fully_empty_tmt_sets" "replace_empty_with_na" "replace_na_with_empty"
# [21] "check_metadata_integers" "syn_empty_channels" "triv_optcols_at_empty" "recheck_tmt_channels"
# [25] "check_tmt_rawfiles" "check_tmt_sampleids" "check_tmt_emptyids" "check_tmt_chans_vs_levs"
# [29] "check_tmt_mixplexes" "check_dups_at_lcms_and_sid" "check_lfq_exptraws" "load_dbs"
# [33] "load_expts" "reload_expts" "channelInfo" "n_TMT_sets"
# [37] "n_LCMS" "TMT_plex" "TMT_plex2" "TMT_levels"
# [41] "simple_label_scheme" "find_mascot_tmtplex"
#
# $nmf.R
# [1] "analNMF" "plotNMFCon" "plotNMFCoef" "plotNMFmeta" "anal_pepNMF" "anal_prnNMF"
# [7] "plot_pepNMFCon" "plot_prnNMFCon" "plot_pepNMFCoef" "plot_prnNMFCoef" "plot_metaNMF"
#
# $normalization.R
# [1] "find_fit_nms" "hfind_fit_nms" "calc_sd_fcts" "center_df" "add_mean_dev" "find_n_comp"
# [7] "my_which_max" "ok_file_ncomp" "spline_coefs" "normMulGau" "dblTrim" "sumdnorm"
# [13] " wt_dnorm" "normSD" "fitKernelDensity" "nmix_params"
#
# $outliers.R
# [1] "locate_outliers" "dixon_test" "q_dixon" "p_dixon" "q_table" "Dixon_outliers"
# [7] "Grubbs_outliers" "grubbs_test" "q_grubbs" " f" "p_grubbs" "Rosner_outliers"
#
# $pca.R
# [1] "plotPCA" "scorePCA" "pepPCA" "prnPCA"
#
# $peptable.R
# [1] "newColnames" "hsubColnames" "use_mq_peptable" "single_mq_prntable" "check_mq_df"
# [6] "extract_mq_ints" " calc_mq_log2r" "pep_mq_lfq" "pep_mq_lfq2" "calc_lfq_log2r"
# [11] "na_single_lfq" "calclfqPepNums" "calclfqPepInts" "spreadPepNums" "aggrNumLCMS"
# [16] "pad_grp_samples" "rep_ls_groups" "normPep_Mplex" "med_summarise_keys" "load_prior"
# [21] "fmt_num_cols" "mergePep" "standPep" "Pep2Prn" "map_peps_prots"
# [26] "find_prot_family_rows" "my_sum_n" "calc_lfq_prnnums" "calc_tmt_prnnums" "pep_to_prn"
# [31] "assign_duppeps" "replace_by_rowone"
#
# $prntable.R
# [1] "standPrn"
#
# $proteoQ.R
# character(0)
#
# $psmtable.R
# [1] "extract_raws"
# [2] "find_mascot_psmraws <-function(filelist = NULL, dat_dir = NULL)"
# [3] "find_mq_psmraws"
# [4] "find_sm_psmraws"
# [5] "find_mf_psmraws"
# [6] "find_pq_psmraws"
# [7] "extract_psm_raws"
# [8] "set_mascot_colnms"
# [9] "batchPSMheader"
# [10] "rmPSMHeaders"
# [11] "add_mod_conf"
# [12] "find_mascot_vmods"
# [13] "add_mascot_pepseqmod"
# [14] "add_empai"
# [15] "add_quality_cols"
# [16] "psm_msplit"
# [17] "find_shared_prots"
# [18] "hfind_shared_prots"
# [19] "add_shared_genes"
# [20] "add_shared_prot_accs_mf"
# [21] "add_shared_sm_genes"
# [22] "procPSMs"
# [23] "check_raws"
# [24] "splitPSM"
# [25] "find_mascot_plex"
# [26] "make_mascot_ratios"
# [27] "make_mascot_intensities"
# [28] "add_mascot_raw"
# [29] "pad_mascot_channels"
# [30] "pad_mascot_fields"
# [31] "psm_mcleanup"
# [32] "cleanupPSM"
# [33] "mcPSM"
# [34] "annotPSM"
# [35] "normPSM"
# [36] "rm_cols_mqpsm"
# [37] "calcPeptide"
# [38] "psm_to_pep"
# [39] "PSM2Pep"
# [40] "my_tolower"
# [41] "my_upper"
# [42] "add_maxquant_pepseqmod"
# [43] "add_msfragger_pepseqmod"
# [44] "add_cols_at"
# [45] "replace_cols_at"
# [46] "reloc_col"
# [47] "reloc_col_after"
# [48] "reloc_col_after_last"
# [49] "reloc_col_after_first"
# [50] "reloc_col_before"
# [51] "reloc_col_before_last"
# [52] "reloc_col_before_first"
# [53] "find_preceding_colnm"
# [54] "order_psm_cols"
# [55] "order_mascot_psm_cols"
# [56] "pad_mq_channels"
# [57] "splitPSM_mq"
# [58] "pad_sm_channels"
# [59] "add_sm_pepseqmod"
# [60] "splitPSM_sm"
# [61] "pad_mf_channels"
# [62] "splitPSM_mf"
# [63] "find_padding_pos"
# [64] "pad_tmt_channels"
# [65] "pad_psm_fields"
# [66] "add_pepseqmod"
# [67] "check_dup_unimods"
# [68] "splitPSM_pq"
# [69] "add_pep_retsd"
# [70] "calc_pep_retsd"
# [71] "add_n_pepexpz"
#
# $purge.R
# [1] "lgl_cleanup" "purge_by_cv" "purge_by_qt" "purge_by_n" "psm_mpurge" "purgePSM" "purgePep"
#
# $roadmap.R
# character(0)
#
# $sigtests.R
# [1] "rowVars" "filterData" "prepFml" "my_padj" "lm_summary" "model_onechannel"
# [7] "sigTest" "pepSig" "prnSig"
#
# $simulData.R
# [1] "simulUniprotPSM" "mascot_refseq2uniprot" "maxquant_refseq2uniprot"
#
# $specialty.R
# [1] "labEffPSM" "procTMT0" "calcTMTLabs" "proteo_hm"
#
# $string.R
# [1] "annot_stringdb" "stringTest" "anal_prnString" "prepString" "load_stringdbs"
#
# $trends.R
# [1] "checkdots_analTrend" "analTrend" "plotTrend" "anal_prnTrend" "plot_prnTrend"
#
# $utils.R
# [1] "prepDM" "find_NorZ" "replace_NorZ_names" "`names_pos<-`"
# [5] "reorder_files" "reorderCols" "reorderCols2" "ins_cols_after"
# [9] "sort_tmt_lcms" "na_zeroIntensity" "not_allzero_rows" "aggrNums"
# [13] "aggrTopn" "aggrLFQs" "tmt_wtmean" " my_trim"
# [17] " my_wtmean" "TMT_top_n" "not_all_zero" "not_all_NA"
# [21] "not_all_nan" "is_all_nan" "is_trivial_col" "is_trivial_dbl"
# [25] "replace_trivial_with_na" "colAnnot" "setHMColor" "setHMlims"
# [29] "ratio_toCtrl" "imputeNA" " my_mice" " handleNA"
# [33] "pepImp" "prnImp" "sp_lookup" "taxid_lookup"
# [37] "taxid_lookup_rev" "sp_lookup_Ul" "add_refseq_gene" "add_entrez"
# [41] "add_custom_entrez" "parse_acc" "parse_fasta" "hparse_fasta"
# [45] "na_genes_by_acc" "na_species_by_org" "add_fasta_attrs" "add_prot_desc"
# [49] "annotPrn" " na_fasta_name_by_prot_acc" " na_acc_type_to_other" "annotKin"
# [53] "save_call" "match_fmls" "match_call_arg" "match_gset_nms"
# [57] "#' foo" "match_logi_gv" "match_prnSig_scale_log2r" "match_pepSig_scale_log2r"
# [61] "replace_na_genes" "na_genes_by_acc" "find_pep_pos" "annotPeppos"
# [65] "subset_fasta" "add_prot_icover" "calc_cover" "to_linfc"
# [69] "rm_sglval_cols" "cmbn_meta" "gg_imgname" "rm_pval_whitespace"
# [73] "filters_in_call" "arrangers_in_call" "calc_sd_fcts_psm" "calcSD_Splex"
# [77] "sd_violin" "rptr_violin" "my_geomean" "count_phosphopeps"
# [81] "count_pepmiss" "contain_str" "contain_chars_in" "not_contain_str"
# [85] "not_contain_chars_in" "start_with_str" "end_with_str" "start_with_chars_in"
# [89] "ends_with_chars_in" "rows_are_all" "rows_are_not_all" "concat_fml_dots"
# [93] "gn_rollup" "identical_dots" "my_complete_cases" "my_union"
# [97] "find_fn_bases" "find_fn_exts" "check_dots" "check_depreciated_args"
# [101] "to_complete_cases" "check_gset_nms" "ok_existing_params" "env_where"
# [105] "set_cutpoints" "set_cutpoints2" "load_craps" "find_int_cols"
# [109] "find_ratio_cols" "make_mq_meta" "make_mq_meta2" " update_nodes"
# [113] "add_entry_ids" "check_formalArgs" "check_formalArgs2" "set_ggsave_dots"
# [117] "find_search_engine" "check_ggplot_aes" "prep_range" "find_delim"
# [121] "recur_flatten" "subset_keepattr" "list_to_dataframe" "find_psmQ_files"
# [125] "get_col_types" "write_excel_wb" "load_ls_group" "parse_col_select"
# [129] "parse_filename" "procBrukerMGF" "procBrukerMGF_v1" "mprocBrukerMGF"
# [133] "check_aes_length"
#
# $utils_proteom.R
# [1] "find_mod_indexesQ" "deduce_mod_indexes" "hdeduce_mod_indexes"
#
# $volcanos.R
# [1] "plotVolcano" "pval_complete_cases" "byfml_volcano" "byfile_plotVolcano" "subset_volcano_df"
# [6] "fullVolcano" "summ_venn" "plot_venn" "gsVolcano" "pepVol"
# [11] "prnVol" "gspaMap" "geom_table" "to_csv_"
#
# $wrappers.R
# [1] "my_dist" "cos_sim"
#
# $zzz.R
# [1] ".onAttach"
#
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