EnsEMBL::Web::Object::Location

Location: /modules/EnsEMBL/Web/Object/Location.pm
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Overview

Bio::ensembl::variation::ldfeaturecontainer

Individual_genotype_table_calls

Individual_table_calls

Information_panel

Method

Unknown

  • _create_DnaAlignFeature
  • _create_Gene
  • _create_OligoFeature
  • _create_ProteinAlignFeature
  • _create_RegulatoryFactor
  • _create_Xref
  • _create_XrefArray
  • _filename
  • _generic_create
  • align_species
  • attach_slice
  • availability
  • can_export
  • caption
  • centrepoint
  • chromosome
  • coord_systems
  • counts
  • create_UserDataFeature
  • create_features
  • current_pop_name
  • generate_query_hash
  • getVariationsOnSlice
  • get_all_misc_sets
  • get_genotyped_VariationsOnSlice
  • get_snp
  • get_source
  • get_synteny_matches
  • length
  • misc_set_code
  • name
  • raw_feature_strand
  • real_species
  • retrieve_DnaAlignFeature
  • retrieve_Gene
  • retrieve_OligoProbe
  • retrieve_ProteinAlignFeature
  • retrieve_RegulatoryFactor
  • retrieve_Transcript
  • retrieve_Xref
  • retrieve_features
  • retrieve_userdata
  • seq_region_end
  • seq_region_length
  • seq_region_name
  • seq_region_start
  • seq_region_strand
  • seq_region_type
  • setCentrePoint
  • setLength
  • short_caption
  • slice
  • slice_cache
  • strand
  • sub_type
  • synonym
Documentation coverage: 26 %

Methods

    addContext



    View source

    extra_pop
    ALSO IN SNP DATA OBJ
    Arg1 Bio::EnsEMBL::Variation::Population object
    Arg[2] Arg[2] : string "super", "sub" Example : $genotype_freq = $self->DataObj->extra_pop($pop, "super");
    Description gets any super/sub populations Returns String
    Returns String
    View source

    focus
    Information_panel.
    Description adds pair of values (type of focus e.g gene or snp and the ID) to panel if the paramater "gene" or "snp" is defined
    Purpose outputs focus of page e.g.. gene, SNP (rs5050)or slice

    View source

    format_pop
    Arg1 population object
    Description returns population info for the given population obj Returns hashref
    Example my $data = $self->format_pop
    Returns hashref
    View source

    get_all_genotypes
    Calls for LD view
    View source

    get_default_pop_name
    Description returns population id for default population for this species Returns population dbID
    Example my $pop_id = $self->DataObj->get_default_pop_name
    Returns population dbID
    View source

    get_synteny_local_genes



    View source

    get_variation_features
    Description gets the Variation features found on a slice Returns Arrayref of Bio::EnsEMBL::Variation::VariationFeatures
    Example my @vari_features = $self->get_variation_features;
    Returns Arrayref of Bio::EnsEMBL::Variation::VariationFeatures
    View source

    individual_genotypes
    Individual_table_calls.
    Arg1 variation feature object
    Description gets Individual Genotype data for this variation Returns hashref with all the data
    Example my $ind_genotypes = $object->individual_table;
    Returns hashref with all the data
    View source

    ld_for_slice
    Arg1 population object (optional)
    Arg2 width for the slice (optional)
    Description returns all LD values on this slice as a Bio::EnsEMBL::Variation::LDFeatureContainer
    Example my $container = $self->ld_for_slice;
    Returns Bio::EnsEMBL::Variation::LDFeatureContainer
    Returns : Bio::EnsEMBL::Variation::LDFeatureContainer
    View source

    location
    Arg1 : (optional) String Name of slice
    Description getter/setter for slice name Returns String for slice name
    Example my $location = $self->DataObj->name;
    Returns String for slice name
    View source

    parent
    Individual_genotype_table_calls.
    Arg2 string "mother" "father" Example : $mother = $object->parent($individual, "mother");
    Args1 Bio::EnsEMBL::Variation::Individual object
    Description gets name of parent if known Returns string (name of parent if known, else 0)
    Returns string (name of parent if known, else 0)
    View source

    pop_description
    Arg1 Bio::EnsEMBL::Variation::Population object Example : $genotype_freq = $self->DataObj->pop_description($pop);
    Description gets the Population description Returns String
    Returns String
    View source

    pop_links
    Arg1 Bio::EnsEMBL::Variation::Population object Example : $genotype_freq = $self->DataObj->pop_links($pop);
    Description gets the Population description Returns String
    Returns String
    View source

    pop_name
    Arg1 Bio::EnsEMBL::Variation::Population object Example : $self->DataObj->pop_name($pop);
    Description gets the Population name Returns String
    Returns String
    View source

    pop_name_from_id
    Arg1 Population id
    Description returns population name as string Returns string
    Example my $pop_name = $self->DataObj->pop_name_from_id($pop_id);
    Returns string
    View source

    pop_obj_from_name
    Arg1 Population name
    Description returns population info for the given population name Returns population object
    Example my $pop_name = $self->DataObj->pop_obj_from_name($pop_id);
    Returns population object
    View source

    pop_size
    Arg1 Bio::EnsEMBL::Variation::Population object Example : $genotype_freq = $self->DataObj->pop_size($pop);
    Description gets the Population size Returns String
    Returns String
    View source

    pops_for_slice
    Description returns all population IDs with LD data for this slice Returns hashref of population dbIDs
    Example my $data = $self->DataObj->ld_for_slice;
    Returns hashref of population dbIDs
    View source

    unmapped_object



    View source


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