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prozor

• 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.

An HTML version of the package documentation can be found here:

https://protviz.github.io/prozor

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("remotes")
remotes::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(devtools)
document()

Example for creating a fasta file with the fgcz_create_fasta.R script

Go to fgcz-r-035.uzh.ch

ls ./fasta_db/p3071_Chlorella
more ./fasta_db/p3071_Chlorella/annotation.txt
more ./fasta_db/p3071_Chlorella/uniprot-taxonomy_3071.fasta
clear
/usr/local/lib/R/site-library/prozor/script/fgcz_create_fasta.R -h

/usr/local/lib/R/site-library/prozor/script/fgcz_create_fasta.R nodecoy ./fasta_db/p3071_Chlorella -o /srv/www/htdocs/FASTA/
/usr/local/lib/R/site-library/prozor/script/fgcz_create_fasta.R ./fasta_db/p3071_Chlorella -o /srv/www/htdocs/FASTA/

cat p3071_Chlorella_d.txt
cat p3071_Chlorella_d.txt | bfabric_save_fasta.py 3071  /srv/www/htdocs/FASTA/fgcz_3071_Chlorella_d_20200604.fasta
# 3071 is the bfabric project name

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.