Files in qzhang503/proteoQ

Processing and Informatic Analysis of Mass Spectrometrirc Data

CODE_OF_CONDUCT.md LICENSE.md R/cluego_api.R R/corrplots.R R/datasets.R R/dbs.R R/funs.R R/global.R R/go.R R/gsea.R R/gspa.R R/gsva.R R/histo.R R/hm.R R/informatics.R R/kin.R R/lda.R R/mds.R R/metadata.R R/nmf.R R/normalization.R R/outliers.R R/pca.R R/peptable.R R/prntable.R R/proteoQ.R R/psmtable.R R/purge.R R/roadmap.R R/sigtests.R R/simulData.R R/specialty.R R/string.R R/trends.R R/utils.R R/utils_mzion.R R/volcanos.R R/wrappers.R R/zzz.R README.md data-raw/additional_sigtest_setups.R data-raw/annotProteinAccession.R inst/extdata/cpp1.R inst/extdata/examples/KinSub_.R inst/extdata/examples/PSM2Pep_.R inst/extdata/examples/Pep2Prn_.R inst/extdata/examples/load_expts_.R inst/extdata/examples/mergePep_.R inst/extdata/examples/normPSM_.R inst/extdata/examples/normPep_.R inst/extdata/examples/normPrn_.R inst/extdata/examples/prepEntrez_.R inst/extdata/examples/prnCorr_.R inst/extdata/examples/prnEucDist_.R inst/extdata/examples/prnGSEA_.R inst/extdata/examples/prnGSPAHM_.R inst/extdata/examples/prnGSPA_.R inst/extdata/examples/prnGSVA_.R inst/extdata/examples/prnHM_.R inst/extdata/examples/prnHist_.R inst/extdata/examples/prnLDA_.R inst/extdata/examples/prnMDS_.R inst/extdata/examples/prnNMF_.R inst/extdata/examples/prnPCA_.R inst/extdata/examples/prnSig_.R inst/extdata/examples/prnString_.R inst/extdata/examples/prnTrend_.R inst/extdata/examples/prnVol_.R inst/extdata/examples/purgePSM_.R inst/extdata/examples/purgePep_.R inst/extdata/workflow_lfq_base.R inst/extdata/workflow_tmt_base.R inst/extdata/workflow_tmt_ext.R man/Dixon_outliers.Rd man/Grubbs_outliers.Rd man/KinSubTest.Rd man/PSM2Pep.Rd man/Pep2Prn.Rd man/Rosner_outliers.Rd man/TMT_levels.Rd man/TMT_plex.Rd man/TMT_plex2.Rd man/TMT_top_n.Rd man/Uni2Entrez.Rd man/aa_residues.Rd man/addMBRpeps.Rd man/add_col_rawfile.Rd man/add_cols_at.Rd man/add_custom_entrez.Rd man/add_empai.Rd man/add_entrez.Rd man/add_entry_ids.Rd man/add_fasta_attrs.Rd man/add_mascot_pepseqmod.Rd man/add_mascot_raw.Rd man/add_maxquant_pepseqmod.Rd man/add_mbr_psms.Rd man/add_mean_dev.Rd man/add_mod_conf.Rd man/add_msfragger_pepseqmod.Rd man/add_msgf_pepseqmod.Rd man/add_n_pepexpz.Rd man/add_pep_n_apexes.Rd man/add_pep_retsd.Rd man/add_pepseqmod.Rd man/add_prot_desc.Rd man/add_prot_icover.Rd man/add_psm_apexes.Rd man/add_quality_cols.Rd man/add_refseq_gene.Rd man/add_scan_id.Rd man/add_shared_genes.Rd man/add_shared_prot_accs_mf.Rd man/add_shared_sm_genes.Rd man/add_sm_pepseqmod.Rd man/aggrLFQs.Rd man/aggrNumLCMS.Rd man/aggrNums.Rd man/aggrTopn.Rd man/alignPSMApexs.Rd man/analNMF.Rd man/analTrend.Rd man/anal_KinSub.Rd man/anal_pepNMF.Rd man/anal_prnString.Rd man/anal_prnTrend.Rd man/annotKin.Rd man/annotPSM.Rd man/annotPeppos.Rd man/annotPrn.Rd man/annot_KinSub.Rd man/annot_from_to.Rd man/annot_stringdb.Rd man/arrangers_in_call.Rd man/assign_duppeps.Rd man/batchPSMheader.Rd man/byfile_gspahm.Rd man/byfile_plotVolcano.Rd man/byfml_gspahm.Rd man/byfml_volcano.Rd man/c2_msig_hs.Rd man/c2_msig_mm.Rd man/c2_msig_rn.Rd man/calcLFQPeptide.Rd man/calcLFQprnnums.Rd man/calcSD_Splex.Rd man/calcTMTLabs.Rd man/calcTMTPeptide.Rd man/calc_avgpep.Rd man/calc_cover.Rd man/calc_lfq_log2r.Rd man/calc_mq_log2r.Rd man/calc_pep_retsd.Rd man/calc_sd_fcts.Rd man/calc_sd_fcts_psm.Rd man/calc_tmt_prnnums.Rd man/calclfqPepInts.Rd man/calclfqPepNums.Rd man/calibPSMApexs2.Rd man/center_df.Rd man/channelInfo.Rd man/check_aes_length.Rd man/check_channel_prefix.Rd man/check_depreciated_args.Rd man/check_dots.Rd man/check_dup_unimods.Rd man/check_dups_at_lcms_and_sid.Rd man/check_empty_rows.Rd man/check_exptfrac_raws.Rd man/check_formalArgs.Rd man/check_formalArgs2.Rd man/check_frac_multipsms.Rd man/check_ggplot_aes.Rd man/check_gset_nms.Rd man/check_lfq_exptraws.Rd man/check_metadata_integers.Rd man/check_mq_df.Rd man/check_optional_cols.Rd man/check_raws.Rd man/check_required_cols.Rd man/check_tmt126_row.Rd man/check_tmt_chans_vs_levs.Rd man/check_tmt_emptyids.Rd man/check_tmt_mixplexes.Rd man/check_tmt_nc.Rd man/check_tmt_plex.Rd man/check_tmt_rawfiles.Rd man/check_tmt_ref.Rd man/check_tmt_sampleids.Rd man/check_unnamed_cols.Rd man/checkdots_analTrend.Rd man/cleanPSMRT_by_sets.Rd man/cleanRTChim.Rd man/cleanupPSM.Rd man/cluego.Rd man/cmbn_meta.Rd man/colAnnot.Rd man/collapse_psm_charges.Rd man/compile_hdr_mods.Rd man/concat_fml_dots.Rd man/contain_str.Rd man/cos_sim.Rd man/count_pepmiss.Rd man/count_phosphopeps.Rd man/create_db_path.Rd man/create_os_lookup.Rd man/dblTrim.Rd man/deduce_mod_indexes.Rd man/dixon_test.Rd man/dl_msig.Rd man/env_where.Rd man/extract_mq_ints.Rd man/extract_psm_raws.Rd man/extract_raws.Rd man/fillMFprnnums.Rd man/fillMQprnnums.Rd man/filterData.Rd man/filters_in_call.Rd man/find_NorZ.Rd man/find_abbr_species.Rd man/find_best_mbry.Rd man/find_delim.Rd man/find_fit_nms.Rd man/find_fn_bases.Rd man/find_fn_exts.Rd man/find_human_orthologs.Rd man/find_int_cols.Rd man/find_mascot_plex.Rd man/find_mascot_psmraws.Rd man/find_mascot_tmtplex.Rd man/find_mascot_vmods.Rd man/find_mbr_int.Rd man/find_mbr_ms1files.Rd man/find_mf_psmraws.Rd man/find_mod_indexesQ.Rd man/find_mq_psmraws.Rd man/find_n_comp.Rd man/find_padding_pos.Rd man/find_path_ms1.Rd man/find_pep_pos.Rd man/find_pq_psmraws.Rd man/find_preceding_colnm.Rd man/find_pri_df.Rd man/find_prot_family_rows.Rd man/find_psmQ_files.Rd man/find_ratio_cols.Rd man/find_search_engine.Rd man/find_sec_df.Rd man/find_shared_prots.Rd man/find_sm_psmraws.Rd man/fitKernelDensity.Rd man/fitMS1RT.Rd man/fixBrukerMGF.Rd man/fml2mass.Rd man/fml_gsea.Rd man/fml_gspa.Rd man/fmt_num_cols.Rd man/fullVolcano.Rd man/geom_lower_text.Rd man/geom_table.Rd man/get_col_types.Rd man/get_full_entrez.Rd man/get_gl_dat_dir.Rd man/gg_imgname.Rd man/gn_rollup.Rd man/go_sets_hs.Rd man/go_sets_mm.Rd man/go_sets_rn.Rd man/greedysetcover.Rd man/groupMZPSM0.Rd man/groupMZPSM1.Rd man/groupMZPepZ.Rd man/grubbs_test.Rd man/gsVolcano.Rd man/gspaHM.Rd man/gspaMap.Rd man/gspaTest.Rd man/gspa_colAnnot.Rd man/gspa_summary_limma.Rd man/gspa_summary_mean.Rd man/gsvaTest.Rd man/hadd_psm_apexes.Rd man/hdeduce_mod_indexes.Rd man/hfind_fit_nms.Rd man/hfind_shared_prots.Rd man/hparse_fasta.Rd man/hpeptideMBR.Rd man/hsubColnames.Rd man/hsub_by_bestz.Rd man/identical_dots.Rd man/impPepNA.Rd man/imputeNA.Rd man/info_anal.Rd man/ins_cols_after.Rd man/is_all_nan.Rd man/is_trivial_col.Rd man/is_trivial_dbl.Rd man/join_mgfs.Rd man/keep_psm_bestint.Rd man/kegg_sets_hs.Rd man/kegg_sets_mm.Rd man/kegg_sets_rn.Rd man/kinase_lookup.Rd man/kinsub_hs.Rd man/kinsub_mm.Rd man/kinsub_rn.Rd man/labEffPSM.Rd man/lgl_cleanup.Rd man/list_to_dataframe.Rd man/lm_gspa.Rd man/lm_summary.Rd man/load_craps.Rd man/load_dbs.Rd man/load_expts.Rd man/load_fasta.Rd man/load_ls_group.Rd man/load_prior.Rd man/load_psmC.Rd man/load_stringdbs.Rd man/locate_outliers.Rd man/makeLFQXYTS.Rd man/make_cls.Rd man/make_frac_smry.Rd man/make_gct.Rd man/make_mascot_intensities.Rd man/make_mascot_ratios.Rd man/make_mq_meta.Rd man/make_mq_meta2.Rd man/map_essential.Rd man/map_peps_prots.Rd man/map_to_entrez.Rd man/map_to_entrez_os_name.Rd man/mart_hs.Rd man/mart_mm.Rd man/mart_rn.Rd man/mascot_refseq2uniprot.Rd man/match_call_arg.Rd man/match_fmls.Rd man/match_gset_nms.Rd man/match_logi_gv.Rd man/match_pepSig_scale_log2r.Rd man/match_prnSig_scale_log2r.Rd man/maxquant_refseq2uniprot.Rd man/mcPSM.Rd man/med_summarise_keys.Rd man/mergePep.Rd man/mfixBrukerMGF.Rd man/mmbr_psms.Rd man/model_onechannel.Rd man/mprocBrukerMGF.Rd man/mq_mods.Rd man/msubsetBrukerMGF.Rd man/my_complete_cases.Rd man/my_custom_cor.Rd man/my_dist.Rd man/my_geomean.Rd man/my_padj.Rd man/my_pheatmap.Rd man/my_sum_n.Rd man/my_tolower.Rd man/my_union.Rd man/my_upper.Rd man/my_which_max.Rd man/n_LCMS.Rd man/n_TMT_sets.Rd man/na_genes_by_acc.Rd man/na_single_lfq.Rd man/na_species_by_org.Rd man/na_zeroIntensity.Rd man/names_pos-set.Rd man/newColnames.Rd man/nmix_params.Rd man/normMulGau.Rd man/normPSM.Rd man/normPep.Rd man/normSD.Rd man/not_all_NA.Rd man/not_all_nan.Rd man/not_all_zero.Rd man/not_allzero_rows.Rd man/ok_existing_params.Rd man/ok_file_ncomp.Rd man/ok_min_size.Rd man/order_mascot_psm_cols.Rd man/order_psm_cols.Rd man/p_dixon.Rd man/p_grubbs.Rd man/pad_grp_samples.Rd man/pad_mascot_channels.Rd man/pad_mascot_fields.Rd man/pad_mf_channels.Rd man/pad_mq_channels.Rd man/pad_psm_fields.Rd man/pad_sm_channels.Rd man/pad_tmt_channels.Rd man/parse_acc.Rd man/parse_col_select.Rd man/parse_fasta.Rd man/parse_filename.Rd man/pep_mf_lfq.Rd man/pep_mq_lfq.Rd man/pep_to_prn.Rd man/peptideMBR.Rd man/plotCorr.Rd man/plotEucDist.Rd man/plotHM.Rd man/plotHisto.Rd man/plotLDA.Rd man/plotMDS.Rd man/plotNMFCoef.Rd man/plotNMFCon.Rd man/plotNMFmeta.Rd man/plotPCA.Rd man/plotTrend.Rd man/plotVolcano.Rd man/plot_corr_sub.Rd man/plot_metaNMF.Rd man/plot_pepNMFCon.Rd man/plot_prnTrend.Rd man/plot_venn.Rd man/pre_mq_meta.Rd man/prepDM.Rd man/prepFml.Rd man/prepGO.Rd man/prepMSig.Rd man/prepString.Rd man/prep_folded_tdata.Rd man/prep_fraction_scheme.Rd man/prep_gspa.Rd man/prep_label_scheme.Rd man/prep_range.Rd man/prnCorr_logFC.Rd man/prnEucDist.Rd man/prnGSEA.Rd man/prnGSPA.Rd man/prnGSPAHM.Rd man/prnGSVA.Rd man/prnHM.Rd man/prnHist.Rd man/prnLDA.Rd man/prnMDS.Rd man/prnPCA.Rd man/prnSig.Rd man/prnVol.Rd man/prn_annot_crap.Rd man/procBrukerMGF.Rd man/procBrukerMGF_v1.Rd man/procMSGFmods.Rd man/procPSMs.Rd man/procTMT0.Rd man/proc_gaf.Rd man/proc_gmt.Rd man/proc_obo.Rd man/proteoQ.Rd man/proteo_hm.Rd man/psm_mcleanup.Rd man/psm_mpurge.Rd man/psm_msplit.Rd man/psm_to_pep.Rd man/purgePSM.Rd man/purgePep.Rd man/purge_by_cv.Rd man/purge_by_n.Rd man/purge_by_qt.Rd man/pval_complete_cases.Rd man/q_dixon.Rd man/q_grubbs.Rd man/q_table.Rd man/ratio_toCtrl.Rd man/read_fasta.Rd man/read_metadata.Rd man/recheck_tmt_channels.Rd man/recur_flatten.Rd man/refseq_entrez_hs.Rd man/refseq_entrez_mm.Rd man/refseq_entrez_rn.Rd man/reload_expts.Rd man/reloc_col.Rd man/reloc_col_after.Rd man/reloc_col_after_first.Rd man/reloc_col_after_last.Rd man/reloc_col_before.Rd man/reloc_col_before_first.Rd man/reloc_col_before_last.Rd man/reorderCols.Rd man/reorderCols2.Rd man/reorder_files.Rd man/rep_ls_groups.Rd man/replace_NorZ_names.Rd man/replace_by_rowone.Rd man/replace_cols_at.Rd man/replace_empty_with_na.Rd man/replace_na_genes.Rd man/replace_na_with_empty.Rd man/replace_trivial_with_na.Rd man/rmPSMHeaders.Rd man/rm_2RToutliers.Rd man/rm_RToutliers.Rd man/rm_apexrt_outliers.Rd man/rm_cols_mqpsm.Rd man/rm_fully_empty_tmt_sets.Rd man/rm_nRToutliers.Rd man/rm_psm_spikes.Rd man/rm_pval_whitespace.Rd man/rm_sglval_cols.Rd man/round_msfmod_decimals.Rd man/rowVars.Rd man/rptr_violin.Rd man/save_call.Rd man/scoreEucDist.Rd man/scoreLDA.Rd man/scoreMDS.Rd man/scorePCA.Rd man/sd_violin.Rd man/sep_mbrfiles.Rd man/setHMColor.Rd man/setHMlims.Rd man/set_cutpoints.Rd man/set_cutpoints2.Rd man/set_dat_dir.Rd man/set_db_outname.Rd man/set_ggsave_dots.Rd man/set_mascot_colnms.Rd man/sigTest.Rd man/simple_label_scheme.Rd man/simulUniprotPSM.Rd man/smbr_psms.Rd man/sort_tmt_lcms.Rd man/sp_lookup.Rd man/sp_lookup_Ul.Rd man/sp_lookup_go.Rd man/spline_coefs.Rd man/splitPSM_ma.Rd man/splitPSM_mf.Rd man/splitPSM_mq.Rd man/splitPSM_mz.Rd man/spreadPepNums.Rd man/standPep.Rd man/standPrn.Rd man/stringTest.Rd man/sub_by_bestz.Rd man/subsetBrukerMGF.Rd man/subset_fasta.Rd man/subset_keepattr.Rd man/subset_volcano_df.Rd man/sumdnorm.Rd man/summ_venn.Rd man/syn_empty_channels.Rd man/taxid_lookup.Rd man/taxid_lookup_rev.Rd man/tmt_wtmean.Rd man/to_complete_cases.Rd man/to_csv_.Rd man/to_linfc.Rd man/triv_optcols_at_empty.Rd man/uniprot_entrez_hs.Rd man/uniprot_entrez_mm.Rd man/uniprot_entrez_rn.Rd man/uniprot_species.Rd man/update_frac_smry.Rd man/update_nodes.Rd man/use_mf_peptable.Rd man/use_mf_prottable.Rd man/use_mq_peptable.Rd man/use_mq_prottable.Rd man/vararg_secmsg.Rd man/write_excel_wb.Rd man/write_fasta.Rd man/write_metadata.Rd vignettes/README.Rmd vignettes/README.md