get_ld_variants_by_window: Get linkage disequilibrium data for variants

In ramiromagno/ensemblr: R Client for the Ensembl REST API

Get linkage disequilibrium data for variants

Description

Gets linkage disequilibrium data for variants from Ensembl REST API. There are four ways to query, either by:

Genomic window centred on variants:

get_ld_variants_by_window(variant_id, genomic_window_size, ...)

Pairs of variants:

get_ld_variants_by_pair(variant_id1, variant_id2, ...)

Genomic range:

get_ld_variants_by_range(genomic_range, ...)

All pair combinations of variants:

get_ld_variants_by_pair_combn(variant_id, ...)

Usage

get_ld_variants_by_window(
  variant_id,
  genomic_window_size = 500L,
  species_name = "homo_sapiens",
  population = "1000GENOMES:phase_3:CEU",
  d_prime = 0,
  r_squared = 0.05,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

get_ld_variants_by_pair(
  variant_id1,
  variant_id2,
  species_name = "homo_sapiens",
  population = "1000GENOMES:phase_3:CEU",
  d_prime = 0,
  r_squared = 0.05,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

get_ld_variants_by_range(
  genomic_range,
  species_name = "homo_sapiens",
  population = "1000GENOMES:phase_3:CEU",
  d_prime = 0,
  r_squared = 0.05,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

get_ld_variants_by_pair_combn(
  variant_id,
  species_name = "homo_sapiens",
  population = "1000GENOMES:phase_3:CEU",
  d_prime = 0,
  r_squared = 0.05,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

variant_id	Variant identifiers, e.g., 'rs123'. This argument is to be used with either function get_ld_variants_by_window() or get_ld_variants_by_pair_combn(). In the case of get_ld_variants_by_pair_combn() all pairwise combinations of elements of variant_id are used to define pairs of variants for querying. Note that this argument is not the same as variant_id1 or variant_id2, to be used with function get_ld_variants_by_pair.
genomic_window_size	An integer vector specifying the genomic window size in kilobases (kb) around the variant indicated in variant_id. This argument is to be used with function get_ld_variants_by_window(). At the moment, the Ensembl REST API does not allow values greater than 500kb. A window size of 500 means looking 250kb upstream and downstream the variant passed as variant_id. The minimum value for this argument is 1L, not 0L.
species_name	The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Examples: 'homo_sapiens' (human), 'ovis_aries' (Domestic sheep) or 'capra_hircus' (Goat).
population	Population for which to compute linkage disequilibrium. See get_populations on how to find available populations for a species.
d_prime	D' is a measure of linkage disequilibrium. d_prime defines a cut-off threshold: only variants whose D' \ge d_prime are returned.
r_squared	r^2 is a measure of linkage disequilibrium. r_squared defines a cut-off threshold: only variants whose r^2 \ge r_squared are returned. The lower bound for r_squared is 0.05, not 0; the upper bound is 1.
verbose	Whether to be verbose about the http requests and respective responses' status.
warnings	Whether to show warnings.
progress_bar	Whether to show a progress bar.
variant_id1	The first variant of a pair of variants. Used with variant_id2. Note that this argument is not the same as variant_id. This argument is to be used with function get_ld_variants_by_pair().
variant_id2	The second variant of a pair of variants. Used with variant_id1. Note that this argument is not the same as variant_id. This argument is to be used with function get_ld_variants_by_pair().
genomic_range	Genomic range formatted as a string "chr:start..end", e.g., "X:1..10000". Check function genomic_range to easily create these ranges from vectors of start and end positions. This argument is to be used with function get_ld_variants_by_range().

Value

A tibble of 6 variables:

species_name

Ensembl species name: this is the name used internally by Ensembl to uniquely identify a species by name. It is the scientific name but formatted without capitalisation and spacing converted with an underscore, e.g., 'homo_sapiens'.

population

Population for which to compute linkage disequilibrium.

variant_id1

First variant identifier.

variant_id2

Second variant identifier.

d_prime

D' between the two variants.

r_squared

r^2 between the two variants.

Examples

# Retrieve variants in LD by a window size of 1kb:
# 1kb: 500 bp upstream and 500 bp downstream of variant.
get_ld_variants_by_window('rs123', genomic_window_size = 1L)

# Retrieve LD measures for pairs of variants:
get_ld_variants_by_pair(
  variant_id1 = c('rs123', 'rs35439278'),
  variant_id2 = c('rs122', 'rs35174522')
)

# Retrieve variants in LD within a genomic range
get_ld_variants_by_range('7:100000..100500')

# Retrieve all pair combinations of variants in LD
get_ld_variants_by_pair_combn(c('rs6978506', 'rs12718102', 'rs13307200'))

ramiromagno/ensemblr documentation built on Oct. 19, 2023, 11:12 a.m.