Inherits from:
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Overview
Displayed.
Method
- _get_pops_from_param
- _warn_block (EnsEMBL::Web::Component)
- output_lddata
- text_haploview
Unknown
- _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
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 |
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_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
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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 keys | For 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 |
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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 |
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text_haploview
| Format | olumns of family, individual, father, mother, gender, affected status and genotypes |
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