Contents

= {ms-error_rate}[http://mspire.rubyforge.org/projects/ms-error_rate]

An {Mspire}[http://mspire.rubyforge.org] library for calculating or dealing
with error rates.  These may be from target-decoy searches, sample bias
validation, or other sources.  

== Examples

=== Target-Decoy with Mascot

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

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

== Installation

  gem install ms-error_rate

== Copyright

See LICENSE

Version data entries

7 entries across 7 versions & 1 rubygems

Version	Path
ms-error_rate-0.0.13	README.rdoc
ms-error_rate-0.0.12	README.rdoc
ms-error_rate-0.0.11	README.rdoc
ms-error_rate-0.0.10	README.rdoc
ms-error_rate-0.0.9	README.rdoc
ms-error_rate-0.0.8	README.rdoc
ms-error_rate-0.0.7	README.rdoc