NAME

Bio::Chado::NaturalDiversity::Reports

SYNOPSIS

use Bio::Chado::NaturalDiversity::Reports

my $sreport = Bio::Chado::NaturalDiversity::Reports->new;
my $data = $sreport->phenotypes_by_trait($phenotypes);

DESCRIPTION

A collection of functions for formatting Chado stock related data in different data structures which can be useful for passing to different programs and software. Because the Chado stock table is the key for storing samples subjected to genotyping and phenotyping experiments, it interacts with several other Chado modules, such as NaturalDiversity for storing the experiment data, Project for storing the metadata about the experiments, Phenotype for the phenotyping values Genotype for the genotyping values.

This module generates several reports for easier access to such data.

Note that all data reports heavily rely on the Natural Diversity schema. The results in each report may differ based on how the experiment data is stored in the databse.

There is no one correct way of loading phenotyping and genotyping data in this module, however there are some examples for 'best practice' in the GMOD Wiki (http://gmod.org/wiki/Chado_Natural_Diversity_Module)

METHODS

new

Make a new Reports object.

phenotypes_by_trait

Usage: $self->phenotypes_by_trait($phenotype_rs , { %args } )
Desc:  generate a report of phenotype values by trait name/accession
Args:  an arrayref of L<Bio::Chado::Schema::Result::Phenotype::Phenotype> ResultSets
       [optional] list of args to filter the report. Currently supported args are

Ret:   arrayref of tab delimited data