prozor: Minimal Protein Set Explaining Peptide Spectrum Matches
Version 0.2.3

Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating libraries with decoys. Planned is peptide FDR estimation for search results.

Browse man pages Browse package API and functions Browse package files

AuthorWitold Wolski
Date of publication2017-04-20 11:43:20 UTC
MaintainerWitold Wolski <wewolski@gmail.com>
LicenseGPL-3
Version0.2.3
URL https://github.com/protviz/prozor
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("prozor")

Man pages

annotateAHO: annotate peptides using AhoCorasickTrie
annotatePeptides: Annotate peptides with protein ids
annotateVec: annotate vector of petpide sequences against fasta file...
createDecoyDB: create db with decoys and contaminants
filterSequences: Filter for specific residues
greedy: given matrix (columns protein rows peptides), compute minimal...
greedyRes2Matrix: converts result of greedy function to a matrix with 3 columns...
loadContaminantsFasta: load list of contaminant sequences
loadContaminantsNoHumanFasta: load list of contaminant without human sequences
loadHomoSapiensSignalPeptides: load human signal peptides
loadMusMusculusSignalPeptides: load mus musculus signal peptides
makeID: make id for chain in format sp|P30443|1A01_HUMANs25
makeIDUnip: make id for chain compatible with uniprot
pepprot: Table containing peptide information
prepareMatrix: given table of peptide protein assigments generate matrix
protpepmeta: Generated from pepprot using method annotatePeptides
protpepmetashort: Small version of pepprot dataset to speed up computation
prozor: Minimal Protein set Explaining Peptides
readPeptideFasta: wrapper setting the correct parameters
removeSignalPeptide: remove signal peptides from main chain
reverseSeq: create rev sequences to fasta list
writeFasta: write fasta lists into file

Functions

annotateAHO Man page Source code
annotatePeptides Man page Source code
annotateProteinIDGrep Source code
annotateVec Man page Source code
createDecoyDB Man page Source code
filterSequences Man page Source code
getMatchingProteinIDX Source code
greedy Man page Source code
greedy2 Source code
greedyRes2Matrix Man page Source code
loadContaminantsFasta Man page Source code
loadContaminantsNoHumanFasta Man page Source code
loadHomoSapiensSignalPeptides Man page Source code
loadMusMusculusSignalPeptides Man page Source code
makeID Man page Source code
makeIDUnip Man page Source code
makePrecursorID Source code
makesig Source code
matchPepsequence Source code
onAttach Source code
pepprot Man page
prepareMatrix Man page Source code
protpepmeta Man page
protpepmetashort Man page
prozor Man page
prozor-package Man page
readPeptideFasta Man page Source code
removeSignalPeptide Man page Source code
removeZeroRows Source code
reverseSeq Man page Source code
reverseSingleSeq Source code
strReverse Source code
writeFasta Man page Source code Source code

Files

inst
inst/creatingDBs
inst/creatingDBs/specAnnotationMilena.Rmd
inst/creatingDBs/StartWithProzor.Rmd
inst/creatingDBs/CreateDB.Rmd
inst/creatingDBs/fixCont.Rmd
inst/extdata
inst/extdata/fgcz_ContaminantsWithAnnotation.fasta
inst/extdata/fgcz_ContaminantsWithAnnotationNoHuman.fasta
inst/extdata/uniprot_signal_homo_sapiens_9606_23032016.tab.gz
inst/extdata/fgcz_contaminants_20150123.fasta
inst/extdata/uniprot_signal_mus_musculus_29032016.tab.gz
inst/extdata/shortfasta.fasta
inst/extdata/UnimodMappings.txt
inst/extdata/uniprot_taxonomy_Oryctolagus_cuniculus.fasta.gz
inst/extdata/fgcz_contaminants_20130115_patchedWithRespectiveUniprot2.fasta
NAMESPACE
data
data/protpepmeta.tab.gz
data/datalist
data/pepprot.tab.gz
data/protpepmetashort.tab.gz
R
R/prepareMatrix.R
R/removeSignalPeptides.R
R/createDecoyDB.R
R/readFasta.R
R/annotatePeptides.R
R/DeprecatedAnnotatePeptides.R
R/loadContaminantsFasta.R
R/reverseSeq.R
R/greedy.R
R/writeFasta.R
R/hello.R
R/zzz.R
README.md
MD5
DESCRIPTION
man
man/greedy.Rd
man/createDecoyDB.Rd
man/greedyRes2Matrix.Rd
man/writeFasta.Rd
man/filterSequences.Rd
man/annotatePeptides.Rd
man/prepareMatrix.Rd
man/loadContaminantsFasta.Rd
man/removeSignalPeptide.Rd
man/prozor.Rd
man/makeID.Rd
man/readPeptideFasta.Rd
man/loadHomoSapiensSignalPeptides.Rd
man/protpepmetashort.Rd
man/protpepmeta.Rd
man/loadContaminantsNoHumanFasta.Rd
man/annotateAHO.Rd
man/annotateVec.Rd
man/reverseSeq.Rd
man/pepprot.Rd
man/loadMusMusculusSignalPeptides.Rd
man/makeIDUnip.Rd
prozor documentation built on May 19, 2017, 8:33 p.m.