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Region

region.Rd

A collection of studies that are associated with a particular region.

Usage

region(
  region_id,
  include_associations = FALSE,
  include_coloc_pairs = FALSE,
  h4_threshold = 0.8
)

Arguments

region_id

A numeric value specifying the region id

include_associations

A logical value specifying whether to include associations (BETA, SE, P), defaults to FALSE

include_coloc_pairs

A logical value specifying whether to include coloc pairs, defaults to FALSE

h4_threshold

A numeric value specifying the h4 threshold for coloc pairs, defaults to 0.8

Value

A list which contains the following elements:

  • gene: A list containing metadata about the gene, including region, and neighboring genes.

  • coloc_groups: a dataframe containing information about which studies have coloc results for this gene. See below for details.

  • study_extractions: a list of dataframes containing the study extractions for this trait. See below for details.

  • rare_results: (optional) a list of dataframes containing the rare results for this trait

  • coloc_pairs: (optional) a dataframe containing all pairwise coloc results for this trait.

  • variants: a dataframe containing the variants for each associated coloc group or rare group.

See below for details.

Details

The dataframes returned by this function are as follows:

coloc_groups_dataframe

The coloc_groups dataframe contains information about which studies have coloc results. It has the following columns:

  • coloc_group_id: the unique id for this group of colocalised results

  • study_id: the id of the study

  • study_extraction_id: the id of the study extraction

  • variant_id: the id of the SNP

  • ld_block_id: the id of the LD block

  • chr: the chromosome of the SNP

  • bp: the base pair position of the SNP

  • min_p: the minimum p-value related to the study_extraction_id

  • cis_trans: the cis/trans status of the SNP

  • ld_block: the LD block of the SNP

  • display_snp: the display SNP name

  • gene: the gene associated with the SNP

  • gene_id: the id of the gene

  • trait_id: the id of the trait

  • trait_name: the name of the trait

  • trait_category: the category of the trait

  • data_type: the data type of the trait

  • tissue: the tissue of the trait

genes_in_region_dataframe

The genes_in_region dataframe contains information about which genes are in a region. It has the following columns:

  • id: the id of the gene

  • ensembl_id: the ensembl id of the gene

  • gene: the name of the gene

  • description: the description of the gene

  • gene_biotype: the gene biotype

  • chr: the chromosome of the gene

  • start: the start position of the gene

  • stop: the stop position of the gene

  • strand: the strand of the gene

  • source: the source of the gene

study_extractions_dataframe

The study_extractions dataframe contains information about which studies have coloc results. It has the following columns:

  • id: the unique id for this study extraction

  • study_id: the id of the study associated with this study extraction

  • variant_id: the id of the SNP

  • snp: the SNP name

  • ld_block_id: the id of the LD block

  • unique_study_id: the unique id for this study

  • study: the study name

  • file: the file name

  • svg_file: the SVG file name

  • file_with_lbfs: the file name with lbfs

  • chr: the chromosome of the SNP

  • bp: the base pair position of the SNP

  • min_p: the minimum p-value related to the study_extraction_id

  • cis_trans: the cis/trans status of the SNP

  • ld_block: the LD block of the SNP

  • gene: the gene associated with the SNP

  • gene_id: the id of the gene

  • trait_id: the id of the trait

  • trait_name: the name of the trait

  • trait_category: the category of the trait

  • data_type: the data type of the trait

  • tissue: the tissue of the trait

rare_results_dataframe

The rare_results dataframe contains information about which studies have coloc results. It has the following columns:

  • rare_result_group_id: the unique id for this rare result group

  • study_id: the id of the study associated with this rare result

  • study_extraction_id: the id of the study extraction associated with this rare result

  • variant_id: the id of the SNP

  • ld_block_id: the id of the LD block

  • chr: the chromosome of the SNP

  • bp: the base pair position of the SNP

  • min_p: the minimum p-value related to the study_extraction_id

  • display_snp: the display SNP name

  • gene: the gene associated with the SNP

  • gene_id: the id of the gene

  • trait_id: the id of the trait

  • trait_name: the name of the trait

  • trait_category: the category of the trait

  • data_type: the data type of the trait

  • tissue: the tissue of the trait

  • ld_block: the LD block of the SNP

coloc_pairs_dataframe

The coloc_pairs dataframe contains information about which studies have coloc pairs. It has the following columns:

  • study_extraction_a_id: the id of the study extraction associated with this coloc pair

  • study_extraction_b_id: the id of the study extraction associated with this coloc pair

  • ld_block_id: the id of the LD block

  • h3: the h3 value for this coloc pair

  • h4: the h4 value for this coloc pair

  • spurious: whether this coloc pair is spurious

variants_dataframe

The variants dataframe contains variant information that is pulled from the Variant Effect Predictor (VEP) database. It has the following columns, along side many more columns from VEP:

  • id: the id of the SNP

  • gene_id: the id of the gene as predicted by VEP

  • gene: the gene name as predicted by VEP