## ----message=FALSE------------------------------------------------------------ library(immunotation) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("immunotation") ## ----------------------------------------------------------------------------- get_valid_organisms() ## ----------------------------------------------------------------------------- df <- retrieve_chain_lookup_table(organism = "human") DT::datatable(head(df, n=30)) ## ----------------------------------------------------------------------------- DT::datatable(head(human_protein_complex_table, n=30)) ## ----------------------------------------------------------------------------- allele_list1 <- c("A*01:01:01", "A*02:01:01", "B*39:01:01", "B*07:02:01", "C*08:01:01", "C*01:02:01") allele_list2 <- c("DPA1*01:03:01", "DPA1*01:04:01", "DPB1*14:01:01", "DPB1*02:01:02", "DQA1*02:01:01", "DQA1*05:03", "DQB1*02:02:01", "DQB1*06:09:01", "DRA*01:01", "DRB1*10:01:01", "DRB1*14:02:01") ## ----------------------------------------------------------------------------- get_serotypes(allele_list1, mhc_type = "MHC-I") ## ----------------------------------------------------------------------------- get_serotypes(allele_list2, mhc_type = "MHC-II") ## ----------------------------------------------------------------------------- get_mhcpan_input(allele_list1, mhc_class = "MHC-I") ## ----------------------------------------------------------------------------- get_mhcpan_input(allele_list2, mhc_class = "MHC-II") ## ----------------------------------------------------------------------------- get_G_group(allele_list2) ## ----------------------------------------------------------------------------- get_P_group(allele_list1) ## ----------------------------------------------------------------------------- allele_list3 <- c("A*01:01:01", "A*02:01:01", "A*03:01") encode_MAC(allele_list3) ## ----------------------------------------------------------------------------- MAC1 <- "A*01:AYMG" decode_MAC(MAC1) ## ----------------------------------------------------------------------------- sel1 <- query_allele_frequencies(hla_selection = "A*02:01", hla_sample_size_pattern = "bigger_than", hla_sample_size = 10000, standard="g") DT::datatable(sel1) ## ----------------------------------------------------------------------------- sel1b <- query_allele_frequencies(hla_selection = "A*01:01", hla_ethnic = "Asian") DT::datatable(sel1b) ## ----------------------------------------------------------------------------- hla_selection <- build_allele_group("A*01:02") sel1 <- query_allele_frequencies(hla_selection = hla_selection, hla_sample_size_pattern = "bigger_than", hla_sample_size = 200, standard="g") ## ----------------------------------------------------------------------------- haplotype_alleles <- c("A*02:01", "B*", "C*") df <- query_haplotype_frequencies(hla_selection = haplotype_alleles, hla_region = "Europe") DT::datatable(df) ## ----------------------------------------------------------------------------- sel2 <- query_allele_frequencies(hla_locus = "B", hla_population = 1986) DT::datatable(sel2) ## ----------------------------------------------------------------------------- sel2a <- query_allele_frequencies(hla_locus = "B", hla_population = 3089) DT::datatable(sel2a) ## ----------------------------------------------------------------------------- plot_allele_frequency(sel1) ## ----------------------------------------------------------------------------- sel3 <- query_population_detail(1986) DT::datatable(sel3, options = list(scrollX = TRUE)) ## ----------------------------------------------------------------------------- sel4 <- query_population_detail(as.numeric(sel1$population_id)) # only select the first 5 columns to display in table DT::datatable(sel4[1:5], options = list(scrollX = TRUE)) ## ----------------------------------------------------------------------------- sessionInfo()