Man pages for qzhang503/proteoQDA
Data employed in the vignette of the proteoQ package
| copy_crap | Copy 'crpa.fasta' to 'db_path' |
| copy_csv | Copy Mascot '.csv' files |
| copy_expt | Copy an 'expt_smry[...].xlsx' file to 'dat_dir' |
| copy_exptsmry_cmbn | Copy a metadata file 'expt_smry.xlsx' file to 'dat_dir' |
| copy_exptsmry_gtmt | Copy a metadata file 'expt_smry.xlsx' to 'dat_dir' |
| copy_exptsmry_plfq | Copy a metadata file 'expt_smry.xlsx' to 'dat_dir' |
| copy_exptsmry_w2ref | Copy a metadata file 'expt_smry.xlsx' to 'dat_dir' |
| copy_exptsmry_w2w16ref | Copy a metadata file 'expt_smry.xlsx' to 'dat_dir' |
| copy_fasta | Copy 'fasta' files |
| copy_frac | Copy a metadata file 'frac_smry.xlsx' |
| copy_fracsmry_cmbn | Copy a metadata file 'frac_smry.xlsx' to 'dat_dir' |
| copy_fracsmry_gtmt | Copy a metadata file 'frac_smry.xlsx' to 'dat_dir' |
| copy_fracsmry_plfq | Copy a metadata file 'frac_smry.xlsx' to 'dat_dir' |
| copy_mascot_gtmt | Copy Mascot global TMT '.csv' |
| copy_mascot_plfq | Copy Mascot phospho LFQ '.txt' |
| copy_mascot_ptmt | Copy Mascot phospho TMT '.csv' |
| copy_maxquant_gtmt | Copy MaxQuant global TMT '.txt' |
| copy_maxquant_plfq | Copy MaxQuant phospho LFQ '.txt' |
| copy_maxquant_ptmt | Copy MaxQuant phospho TMT '.txt' |
| copy_mgf | Copy '.mgf' files |
| copy_msconv_mgf | Copy MSConvert MGF files. |
| copy_msfragger_gtmt | Copy MSFragger global TMT '.tsv' |
| copy_msfragger_plfq | Copy MSFragger phospho LFQ '.tsv' |
| copy_pd_mgf | Copy Proteome Discoverer MGF files. |
| copy_proteom_gtmt | Copy proteoM global TMT '.txt' |
| copy_proteom_plfq | Copy proteoM phospho LFQ '.txt' |
| copy_refseq_hs | Copy 'refseq_hs_2013_07.fasta' to 'db_path' |
| copy_refseq_mm | Copy 'refseq_mm_2013_07.fasta' to 'db_path' |
| copy_specmill_gtmt | Copy Spectrum Mill global TMT '.ssv' |
| copy_specmill_plfq | Copy Spectrum Mill phospho LFQ '.ssv' |
| copy_specmill_ptmt | Copy Spectrum Mill phospho TMT '.ssv' |
| copy_ssv | Copy Spectrum Mill '.ssv' files |
| copy_tsv | Copy MSFragger '.tsv' files |
| copy_txt | Copy MaxQuant '.txt' files |
| copy_uniprot_hsmm | Copy 'uniprot_hsmm_2020_03.fasta' to 'db_path' |
| F003590 | Mascot global TMT |
| F003591 | Mascot global TMT |
| F003593 | Mascot global TMT |
| F003594 | Mascot global TMT |
| F003595 | Mascot global TMT |
| F003597 | Mascot global TMT |
| F003598 | Mascot phosphopeptide TMT A 'Mascot' PSM table from the... |
| F003602 | Mascot phosphopeptide TMT |
| F003603 | Mascot phosphopeptide TMT |
| F003604 | Mascot phosphopeptide TMT |
| F003605 | Mascot phosphopeptide TMT |
| F003606 | Mascot phosphopeptide TMT |
| F003997_lfq_p | Mascot IMAC data (LFQ) |
| foo_fasta_rda | Save 'fasta' files to '.rda' |
| foo_mascot_fullset | Mascot rda files |
| foo_mascot_lfq | Mascot phospho LFQ rda files |
| foo_mascot_psmidx | Mascot subset rda files |
| foo_mascot_subset | Mascot subset rda files |
| foo_mascot_subset_not_working | Mascot subset rda files |
| foo_mascot_subset_tenperent_na | Mascot subset rda files |
| foo_maxquant_lfq | MaxQuant LFQ rda files |
| foo_mgf | Saves MGFs from MSConvert or Proteome Discoverer to '.rda'. |
| foo_mq_resave | Re-save MaxQuant rda files |
| foo_mq_subset | MaxQuant subset rda files |
| foo_msfragger_lfq | MSFragger LFQ rda files |
| foo_msfragger_tmt_subset | MSFragger TMT rda files |
| foo_proteom_tmt_subset | proteoM TMT rda files |
| foo_sm_lfq | Spectrum Mill LFQ rda files |
| foo_sm_subset | SpectrumMill subset rda files |
| msconv_bi1_imac_partial | MSConvert IMAC TMT |
| msms_bi_1 | MaxQuant global TMT |
| msms_bi_2 | MaxQuant global TMT |
| msms_bi_p1 | MaxQuant phosphopeptide TMT |
| msms_bi_p2 | MaxQuant phosphopeptide TMT |
| msms_jhu_1 | MaxQuant global TMT |
| msms_jhu_2 | MaxQuant global TMT |
| msms_jhu_p1 | MaxQuant phosphopeptide TMT |
| msms_jhu_p2 | MaxQuant phosphopeptide TMT |
| msms_lfq_p | MaxQuant IMAC data (LFQ) |
| msms_pnnl_1 | MaxQuant global TMT |
| msms_pnnl_2 | MaxQuant global TMT |
| msms_pnnl_p1 | MaxQuant phosphopeptide TMT |
| msms_pnnl_p2 | MaxQuant phosphopeptide TMT |
| pd_bi1_gl_partial | Proteome Discoverer (PD) global TMT |
| psm_lfq_bi_p1 | MSFragger IMAC data (LFQ) |
| psm_lfq_bi_p2 | MSFragger IMAC data (LFQ) |
| psm_lfq_jhu_p1 | MSFragger IMAC data (LFQ) |
| psm_lfq_jhu_p2 | MSFragger IMAC data (LFQ) |
| psm_lfq_pnnl_p1 | MSFragger IMAC data (LFQ) |
| psm_lfq_pnnl_p2 | MSFragger IMAC data (LFQ) |
| psmQ_lfq_p | proteoM IMAC data (LFQ) |
| psmQ_tmt_bi_1 | proteoM global TMT |
| psmQ_tmt_bi_2 | proteoM global TMT |
| psmQ_tmt_jhu_1 | proteoM global TMT |
| psmQ_tmt_jhu_2 | proteoM global TMT |
| psmQ_tmt_pnnl_1 | proteoM global TMT |
| psmQ_tmt_pnnl_2 | proteoM global TMT |
| psm_tmt_bi_1 | MSFragger global TMT |
| psm_tmt_bi_2 | MSFragger global TMT |
| psm_tmt_jhu_1 | MSFragger global TMT |
| psm_tmt_jhu_2 | MSFragger global TMT |
| psm_tmt_pnnl_1 | MSFragger global TMT |
| psm_tmt_pnnl_2 | MSFragger global TMT |
| scc_hs | UniProt subcellular locations |
| scc_mm | UniProt subcellular locations |
| scc_rn | UniProt subcellular locations |
