README.md

In protViz/prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

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 ./fasta_db/p3071_Chlorella nodecoy -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

protViz/prozor documentation built on Oct. 17, 2023, 6:39 p.m.