Package: prozor 0.3.4

Witold Wolski

prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants. Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.

Authors:Witold Wolski [aut, cre]

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prozor.pdf |prozor.html✨
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NEWS

# Install 'prozor' in R:
install.packages('prozor', repos = c('https://protviz.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/protviz/prozor/issues

Datasets:
  • bcd - Data frame as produced by COMET-MS search engine
  • fdrSample - Data frame score and proteinID
  • masses - MS masses A dataset containing approx 150000 MS1 precursor masses
  • pepprot - Table containing peptide information
  • protpepmetashort - Small version of pepprot dataset to speed up computation

On CRAN:

softwaremassspectrometryproteomicsexperimenthubsoftware

4.45 score 6 stars 93 scripts 224 downloads 25 exports 44 dependencies

Last updated 11 days agofrom:cce7bcbca4. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 12 2024
R-4.5-winERRORNov 12 2024
R-4.5-linuxERRORNov 12 2024
R-4.4-winERRORNov 12 2024
R-4.4-macERRORNov 12 2024
R-4.3-winERRORNov 12 2024
R-4.3-macERRORNov 12 2024

Exports:annotateAHOannotatePeptidesCdswcomputeFDRcomputeFDRwithIDcreate_fgcz_fasta_dbcreateDecoyDBgreedy_parsimonygreedyRes2Matrixload_special_prot_2024load_universal_contaminants_2024loadContaminantsFasta2019loadContaminantsFasta2021loadContaminantsFGCZ2022make_fasta_summarymakeIDmakeIDUnipplotFDRpredictScoreFDRprepareMatrixreadjustWindowsreadPeptideFastaremoveSignalPeptidereverseSeqwriteFasta

Dependencies:ade4AhoCorasickTriebitbit64clicliprcpp11crayondocoptdplyrfansigenericsgluehmslatticelifecyclemagrittrMASSMatrixnlmepillarpixmappkgconfigprettyunitsprogressprotVizpurrrR6RcppRcppArmadilloreadrrlangsegmentedseqinrspstringistringrtibbletidyselecttzdbutf8vctrsvroomwithr

Readme and manuals

Help Manual

Help pageTopics
annotate peptides using AhoCorasickTrieannotateAHO
Annotate peptides with protein idsannotatePeptides
Data frame as produced by COMET-MS search enginebcd
Compute dynamic swath windowsCdsw Cdsw-class
Compute FDR given a scorecomputeFDR
Compute FDR given a scorecomputeFDRwithID
create fasta db from one or more fasta filescreate_fgcz_fasta_db
Create db with decoys and contaminantscreateDecoyDB
Data frame score and proteinIDfdrSample
given matrix (columns protein rows peptides), compute minimal protein set using greedy algorithmgreedy_parsimony
converts result of greedy_parsimony function to a matrix with 3 columns - peptide - charge and proteingreedyRes2Matrix
load special protload_special_prot_2024
load universal contaminantsload_universal_contaminants_2024
load list of contaminant sequences FGCZ 2019loadContaminantsFasta2019
load list of contaminant sequences FGCZ 2021loadContaminantsFasta2021
load list of contaminant sequences FGCZ 2022loadContaminantsFGCZ2022
make db summary which includes number of sequences, and amino acid statistcismake_fasta_summary
make id for chain in format sp|P30443|1A01_HUMANs25makeID
make id for chain compatible with uniprotmakeIDUnip
MS masses A dataset containing approx 150000 MS1 precursor massesmasses
compute the deviation from optimum: equal number of MS1 per binobjectiveMS1Function
Table containing peptide informationpepprot
plot FDRplotFDR
Predict score given FDRpredictScoreFDR
given table of peptide protein assigments generate matrixprepareMatrix
Small version of pepprot dataset to speed up computationprotpepmetashort
Minimal Protein Set Explaining Peptidesprozor-package prozor
Readjust windows so that boundaries in regions of few peaks.readjustWindows
wrapper setting the correct parameters seqinr::read.fasta for reading peptide sequencesreadPeptideFasta
remove signal peptides from main chainremoveSignalPeptide
create rev sequences to fasta listreverseSeq
write fasta lists into filewriteFasta