ms-error_rate¶ ↑

An Mspire library for calculating or dealing with error rates. These may be from target-decoy searches, sample bias validation, or other sources.

Generate q-values (right now only with Mascot and MascotPercolator):

require 'ms/error_rate/qvalue'
target_hits = Ms::ErrorRate::Qvalue::Mascot.qvalues(target_files, decoy_files)
# target_hit is a PeptideHit Struct (:filename, :query_title, :charge, :sequence, :mowse, :qvalue)

# or on the commandline:
% qvalues.rb <target>.dat <decoy>.dat

The same output can be produced from Mascot-Percolator output:

require 'ms/error_rate/qvalue'
target_hits = Ms::ErrorRate::Qvalue::Mascot::Percolator.qvalues(datp_files, tab_dot_text_files)
# or commandline:
% qvalues.rb <target>.datp <target>.tab.txt

Sample Bias Validation allows error rate determination based on expected biases in sample composition. Here is an example using transmembrane sequence content. We will assume a fasta file called ‘proteins.fasta`:

# create a peptide-centric database
fasta_to_peptide_centric_db.rb proteins.fasta  # defaults 2 missed cleavages, min aaseq 4
   # generates a file: proteins.msd_clvg2.min_aaseq4.yml

# create a transmembrane sequence prediction file
fasta_to_phobius.rb proteins.fasta     # => generates proteins.phobius

generate_sbv_input_hashes.rb proteins.msd_clvg2.min_aaseq4.yml --tm proteins.phobius,1
   # creates two files:
   # proteins.msd_clvg2.min_aaseq4.tm_min1.by_aaseq.yml
   # proteins.msd_clvg2.min_aaseq4.tm_min1.freq_by_length.yml

# cytosolic fraction (transmembrane sequences not expected):
error_rate qvalues.yml --fp-sbv proteins.msd_clvg2.min_aaseq4.tm_min1.by_aaseq.yml,\
    proteins.msd_clvg2.min_aaseq4.tm_min1.freq_by_length.yml,0.05

gem install ms-error_rate

See LICENSE