Bio-EBI-RNAseqAPI

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lib/Bio/EBI/RNAseqAPI.pm  view on Meta::CPAN

);

=back

=head1 METHODS

=head2 Analysis results per sequencing run

These functions take arguments in the form of a hash. These usually
consist of a study accession, or one or more run accessions, plus a value for
"minimum_mapped_reads". This value represents the minimum percentage of mapped
reads to allow for each run in the results. Only information for runs with a
percentage of mapped reads greater than or equal to this value will be
returned. To get all available information, set "minimum_mapped_reads" to zero.

Analysis information for each run is returned in an anonymous hash. Some
functions return anonymous arrays with one anonymous hash per run found. See
below for examples and more information about the results.


=over 2

=item B<get_run>

lib/Bio/EBI/RNAseqAPI.pm  view on Meta::CPAN

=back

=head2 Baseline gene expression per tissue, cell type, developmental stage, sex, and strain

=over 2

=item B<get_expression_by_organism_genesymbol>

Accesses the API's C<getExpression> endpoint. Provide arguments as a hash,
passing an organism name and a gene symbol, as well as a value for the minimum
percentage of mapped reads to allow:

 my $geneExpressionInfo = $rnaseqAPI->get_expression(
    minimum_mapped_reads => 0,
    organism    => "oryza_sativa",
    gene_symbol => "BURP7"
 );

Results are returned as an anonymous array of anonymous hashes, with one
anonymous hash per unique combination of tissue, cell type, developmental
stage, sex, and strain. The median expression level of all runs is given in TPM

lib/Bio/EBI/RNAseqAPI.pm  view on Meta::CPAN

    }
}



=item B<get_expression_by_gene_id>

Accesses the API's C<getExpression> endpoint, but instead of querying by
organism and gene symbol (see L</get_expression_by_organism_genesymbol>), this
function queries by gene identifier. Also expects a value for the minimum
percentage of mapped reads to allow.

 my $geneExpressionInfo = $rnaseqAPI->get_expression(
    gene_identifer  => "ENSG00000172023",
    minimum_mapped_reads => 0
 );

Results are returned as an anonymous array of anonymous hashes, with one
anonymous hash per unique combination of tissue, cell type, developmental
stage, sex, and strain. See L</get_expression_by_organism_genesymbol> for an
example.  The median expression level of all runs is given in TPM (transcripts

lib/Bio/EBI/RNAseqAPI.pm  view on Meta::CPAN

    my ( $self, $args ) = @_;

    my $logger = $self->get_log_writer;

    my $userAgent = $self->get_user_agent;

    # Start building the query URL.
    my $url = $self->get_api_base . "/json/";
    
    # If we're passed a minimum percentage of mapped reads, add this to the URL
    # next.
    if( defined( $args->{ "minimum_mapped_reads" } ) ) {

        $url .= $args->{ "minimum_mapped_reads" } . "/";
    }
    
    # Add the function name and argument to the end of the URL.
    $url .= $args->{ "function_name" };

    if( $args->{ "function_argument" } ) {