MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide
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library(immunotation)
# 1. Retrieve valid organisms and chain lookup table for humans
organisms <- get_valid_organisms()
human_chains <- retrieve_chain_lookup_table(organism = "human")
# 2. Map HLA alleles to serotypes and NetMHCpan inputs
allele_list <- c("A*01:01:01", "A*02:01:01", "B*39:01:01")
serotypes <- get_serotypes(allele_list, mhc_type = "MHC-I")
mhcpan_input <- get_mhcpan_input(allele_list, mhc_class = "MHC-I")
# 3. Query allele frequencies in global populations
freq_data <- query_allele_frequencies(
hla_selection = "A*02:01",
hla_sample_size_pattern = "bigger_than",
hla_sample_size = 10000,
standard = "g"
)
Input/Output Note: Inputs are HLA allele lists and population query parameters; outputs are serotypes, tool-compatible HLA strings, and population frequency tables.
get_serotypes.get_mhcpan_input.get_G_group) or P groups (get_P_group).query_allele_frequencies and query_haplotype_frequencies.plot_allele_frequency.immunotation only formats the inputs)."A*01:01:01")."human", "mouse") used in retrieve_chain_lookup_table."MHC-I" or "MHC-II") used in get_serotypes."MHC-I" or "MHC-II") used in get_mhcpan_input."bigger_than")."g" for Gold, "s" for Silver, "b" for Bronze).get_valid_organisms to check if a species is supported before building a lookup table.get_G_group or get_P_group to resolve ambiguous HLA typings.standard = "g" (Gold standard) to ensure high-quality allele frequency data.NA. Ensure both chains are annotated in the MHC restriction ontology (MRO).HLAtools: For general HLA data manipulation and analysis.还没有评价。欢迎分享你的使用感受。
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