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.


Build Status Project Stats CRAN_Status_Badge Determine minimal Protein set given list of peptide protein mappings. Various weights can be assigned to peptides (i.e. inverse peptide frequencies). Generate reverse decoy sequences

How to install:

For CRAN version (not the newest). Please use the github version.

install.packages("prozor")

This is how you install the github version.

install.packages("devtools")
library(devtools)
install_github("protviz/prozor")

for Developers

downlod git repo. Use roxygenize2 to document new functions. Than run these 2 commands to update namespace and Rd files:

library(prozor)
document()

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Reference manual

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install.packages("prozor")

0.2.11 by Witold Wolski, a year ago


https://github.com/protviz/prozor


Report a bug at https://github.com/protviz/prozor/issues


Browse source code at https://github.com/cran/prozor


Authors: Witold Wolski


Documentation:   PDF Manual  


GPL-3 license


Imports AhoCorasickTrie, Matrix, doParallel, foreach, plyr, readr, seqinr, stringr, dplyr

Suggests knitr, rmarkdown


See at CRAN