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Variants

variants.Rd

Get specific variants from the API. The API accepts variant identifiers (variant_ids, rsids, or strings) and returns collapsed/combined data. The API distinguishes between identifier types automatically. Max 10 variants when expand=TRUE.

Usage

variants(
  variants,
  expand = FALSE,
  include_associations = FALSE,
  include_coloc_pairs = FALSE,
  h4_threshold = 0.8
)

Arguments

variants

A vector of variant identifiers (variant_ids, rsids, or strings)

expand

Logical. FALSE (default) returns minimal data. TRUE returns full VariantResponse (max 10)

include_associations

Logical. Whether to include associations (BETA, SE, P). Only when expand=TRUE

include_coloc_pairs

Logical. Whether to include coloc pairs. Only when expand=TRUE

h4_threshold

Numeric. H4 threshold for coloc pairs, defaults to 0.8

Value

A list which contains the following elements:

  • variants: a dataframe containing the variants for all requested variants

  • coloc_groups: (if expanded) a dataframe containing the coloc groups for all variants

  • study_extractions: (if expanded) a dataframe containing the study extractions for all variants

  • rare_results: (if expanded) a dataframe containing the rare results for all variants

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

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

summary_statistics_dataframe

The summary_statistics dataframe contains information about which studies have summary statistics. From the API, column names are typically uppercase (SNP, CHR, BP, EA, OA, EAF, Z, BETA, SE, P, LBF_1, etc.). It has the following columns (names may be upper or lower case depending on source):

  • SNP / variant_id: the id of the SNP

  • CHR / chr: the chromosome of the SNP

  • BP / bp: the base pair position of the SNP

  • EA / ea: the effect allele

  • OA / oa: the other allele

  • EAF / eaf: the estimated allele frequency

  • Z / z: the z-score

  • BETA / beta: the beta value

  • SE / se: the standard error

  • P / p: the p-value

  • imputed: whether the summary statistics are imputed

  • LBF_* / lbf_*: all different finemapped log-bayes factors for each credible set. Each credible set is numbered from 1 to 10. If finemapped failed or only returned 1 credible set, the LBF_1 column is just converted directly from the z-score.

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