bioconductor-immunotation

name

bioconductor-immunotation

description

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

immunotation

Workflows

Standard Workflow

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_inputallele_list mhc_class  


freq_data  query_allele_frequencies
  hla_selection   
  hla_sample_size_pattern   
  hla_sample_size   
  standard