Boutros Lab Software
and 2 contributors

NAME

        Bio::Sampling::Valection

VERSION

Version 1.0.1

DESCRIPTION

Bio::Sampling::Valection - Sampler for verification

Bio::Sampling::Valection contains a variety of algorithms for choosing verification candidates from competing tools or parameterizations, to fairly assess their performance against each other.

Originally created to selected from single nucleotide variant (SNV) calls generated by SNV mutation calling algorithms, this software can easily be extended to other mutation types (e.g. structural variants, gene fusions, etc.) provided data is formatted correctly.

This software requires the valection package (http://labs.oicr.on.ca/boutros-lab/software/valection).

SYNOPSIS

There are six selection methods available through six functions. They all take the following arguments:

- **budget**: an integer specifying how many candidates to select

- **infile**: a path to a file which contains the calls from all callers. The infile should be formatted with a tab separating the caller and call on each line:

        caller1 name\ta call this caller made
        caller2 name\ta call this caller made

e.g.

        magnifying glass        chr1 576834
        magnifying glass        chr1 6878924
        eye dropper     chr1 496267
        eye dropper     chr1 6878924

Note that the call can contain a tab, but the caller may not.

- **outfile**: a path to a filename where the calls should be outputted

- **seed** (optional): an integer to seed the random number generator with (used to randomize sampling)

        use Bio::Sampling::Valection;

        # Run the sampling to select 10 candidates
        run_equal_per_caller(10, "/home/me/calls.valec", "/home/me/selections.txt", 50);

FUNCTIONS

The functions are named as follows:

run_directed_sampling
run_random_sampling
run_equal_per_caller
run_equal_per_overlap
run_increasing_with_overlap
run_decreasing_with_overlap

AUTHOR

Chris Cooper - Boutros Lab

ACKNOWLEDGEMENTS

Paul Boutros, PhD, PI - Boutros Lab

The Ontario Institute for Cancer Research

COPYRIGHT

This software is copyright (c) 2015 by the Ontario Institute for Cancer Research.