query_allele_frequencies: Query allele frequencies

In imkeller/immunotation: Tools for working with diverse immune genes

Query allele frequencies

Description

Query allele frequencies

Usage

query_allele_frequencies(
  hla_locus = NA,
  hla_selection = NA,
  hla_population = NA,
  hla_country = NA,
  hla_region = NA,
  hla_ethnic = NA,
  hla_sample_size_pattern = NA,
  hla_sample_size = NA,
  standard = "a"
)

Arguments

hla_locus	HLA locus that will be used for filtering data. A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1
hla_selection	Allele that will be used for filtering data. e.g. A*01:01
hla_population	Numeric identifier of the population that will be used for filtering. This identifier is defined by the Allele Frequency Net Database.
hla_country	Country of interest (e.g. Germany, France, ...).
hla_region	Geographic region of interest (e.g. Europe, North Africa, ...)
hla_ethnic	Ethnic origin of interest (e.g. Caucasoid, Siberian, ...)
hla_sample_size_pattern	Keyword used to define the filtering for a specific population size. e.g. "bigger_than", "equal", "less_than", "less_equal_than", "bigger_equal_than"
hla_sample_size	Integer number used to define the filtering for a specific population size, together with the hla_sample_size_pattern argument.
standard	Population standards, as defined in the package vignette. "g" - gold, "s" - silver, "a" - all

Value

data.frame object containing the result of the allele frequency query

Examples

# select frequencies of the A*02:01 allele,
# for gold standard population with more than 10,000 individuals
sel <- query_allele_frequencies(hla_selection = "A*02:01",
hla_sample_size_pattern = "bigger_than", hla_sample_size = 10000,
standard="g")

imkeller/immunotation documentation built on Jan. 3, 2023, 1:31 p.m.