NAME¶
Bio::Chado::NaturalDiversity::Reports - Collection of functions for formatting
Chado stock related data
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