EnsEMBL::Web::Component::LDtable

Location: /modules/EnsEMBL/Web/Component/LDtable.pm
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  • _attach_das (EnsEMBL::Web::Component)
  • _error (EnsEMBL::Web::Component)
  • _export (EnsEMBL::Web::Component)
  • _export_image (EnsEMBL::Web::Component)
  • _get_colour_gradient
  • _hint (EnsEMBL::Web::Component)
  • _info (EnsEMBL::Web::Component)
  • _info_panel (EnsEMBL::Web::Component)
  • _init (EnsEMBL::Web::Component)
  • _matches (EnsEMBL::Web::Component)
  • _sort_similarity_links (EnsEMBL::Web::Component)
  • _warning (EnsEMBL::Web::Component)
  • ajaxable (EnsEMBL::Web::Component)
  • build_sequence (EnsEMBL::Web::Component)
  • cache (EnsEMBL::Web::Component)
  • cache_key (EnsEMBL::Web::Component)
  • cache_print (EnsEMBL::Web::Component)
  • cacheable (EnsEMBL::Web::Component)
  • caption (EnsEMBL::Web::Component)
  • chunked_content (EnsEMBL::Web::Component)
  • configurable (EnsEMBL::Web::Component)
  • excel_lddata
  • get_sequence_data (EnsEMBL::Web::Component)
  • haploview_dump
  • haploview_files
  • html_lddata
  • image_width (EnsEMBL::Web::Component)
  • markup_codons (EnsEMBL::Web::Component)
  • markup_comparisons (EnsEMBL::Web::Component)
  • markup_conservation (EnsEMBL::Web::Component)
  • markup_exons (EnsEMBL::Web::Component)
  • markup_line_numbers (EnsEMBL::Web::Component)
  • markup_variation (EnsEMBL::Web::Component)
  • modal_form (EnsEMBL::Web::Component)
  • new (EnsEMBL::Web::Component)
  • new_image (EnsEMBL::Web::Component)
  • new_karyotype_image (EnsEMBL::Web::Component)
  • new_vimage (EnsEMBL::Web::Component)
  • object (EnsEMBL::Web::Component)
  • remove_redundant_xrefs (EnsEMBL::Web::Component)
  • site_name (EnsEMBL::Web::Component)
  • text_lddata
Documentation coverage: 11 %

Methods

    _get_pops_from_param
    Arg1 Proxy object Gets population names from 'bottom' CGI parameter and puts them into a hash with population names as keys Returns hashref
    Returns hashref
    View source

    _warn_block
    Simple subroutine to dump a formatted "warn" block to the error logs - useful when debugging complex data structures etc... output looks like:



    # # # TEXT. TEXT. TEXT. TEXT. # # TEXT. TEXT. TEXT. TEXT. # # TEXT. TEXT. TEXT. TEXT. # # # # TEXT. TEXT. TEXT. TEXT. # # TEXT. TEXT. TEXT. TEXT. # # #




    Inherited from EnsEMBL::Web::Component
    View source

    ld_values
    Return info : Keys are the type of LD data (r2, dprime)

    Arg1 The data object
    Description Array of pairwise values which can then be formatted to be a table in text, html, excel format etc. Only the bottom left half of the in text, html, excel format etc. Only the bottom left half of the table''s values are filled in to avoid duplicating the data displayed. The last SNP column is not rendered as all pairwise data for this SNP is already displayed elsewhere in the table The first SNP row is not displayed as this would just duplicated data Returns hashref
    Example my $return = ld_values($object);
    For each $return{"r2"} there are two keysFor each $return{"r2"} there are two keys: data, and text The text string is the title for the table
    The data is an array ref with three array refs start postitions, snpnames and the rest of the table data Each value in the array is an arrayrefs with arrayref of SNP start positions in basepair (start order) Arrayref of SNP names in start order Arrayref 2 dimensional array of LD values
    Returns hashref
    View source

    output_lddata
    The arguments are either a string with "No data" message or Arrayref Each value in the array is an arrayrefs with arrayref of SNP start positions in basepair (start order), arrayref of SNP names in start order, Arrayref 2 dimensional array of LD values, Example : $self->excel_ldtable({$title, \@starts, \@snps, \@table});
    Description prints excel formatted table for LD data

    View source

    text_haploview
    Format olumns of family, individual, father, mother, gender, affected status and genotypes

    View source