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hla.R
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hla.R
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# hla.R
# Define HLA Antigen groups
# Randall Johnson
# CCR Collaborative Bioinformatics Resource
# Advanced Biomedical Computing Center at Frederick National Laboratory
# Created January 30, 2015
# Last Modified February 2, 2015
########################
# HLA Class I Antigens #
########################
# this section contains broad splits and associated antigens primarily detectable by serology
# see http://hla.alleles.org/antigens/broads_splits.html for details
tmp <- read.csv('data/hlaA_broad.csv', comment.char = '#', colClasses = 'character')
hlaA.broad <- tmp$broadSpecificity
names(hlaA.broad) <- tmp$alleleGroup
save(hlaA.broad, file = 'HLA/data/hlaA_broad.RData')
tmp <- read.csv('data/hlaB_broad.csv', comment.char = '#', colClasses = 'character')
hlaB.broad <- tmp$broadSpecificity
names(hlaB.broad) <- tmp$alleleGroup
save(hlaB.broad, file = 'HLA/data/hlaB_broad.RData')
tmp <- read.csv('data/hlaC_broad.csv', comment.char = '#', colClasses = 'character')
hlaC.broad <- tmp$broadSpecificity
names(hlaC.broad) <- tmp$alleleGroup
save(hlaC.broad, file = 'HLA/data/hlaC_broad.RData')
#########################
# HLA Class II Antigens #
#########################
# As with the previous section, this section contains broad splits and associated antigens
# see http://hla.alleles.org/antigens/broads_splits.html for details
tmp <- read.csv('data/hlaDRB1_broad.csv', comment.char = '#', colClasses = 'character')
hlaDRB1.broad <- tmp$broadSpecificity
names(hlaDRB1.broad) <- tmp$alleleGroup
save(hlaDRB1.broad, file = 'HLA/data/hlaDRB1_broad.RData')
tmp <- read.csv('data/hlaDQA_broad.csv', comment.char = '#', colClasses = 'character')
hlaDQA.broad <- tmp$broadSpecificity
names(hlaDQA.broad) <- tmp$alleleGroup
save(hlaDQA.broad, file = 'HLA/data/hlaDQA_broad.RData')
################
# HLA B Groups #
################
# this section contains Bw4 and Bw6 assocated specificities (last updated Feb 2, 2015)
# see http://hla.alleles.org/antigens/bw46.html for low resolution details
# and http://www.ufrgs.br/imunovet/molecular_immunology/hla.html for additional details
hlaBw <- read.csv('data/hlaBw.csv', comment.char = '#', stringsAsFactors = FALSE,
na.strings = '')
save(hlaBw, file = 'HLA/data/hlaBw.RData')
################
# HLA C Groups #
################
# this section contains information on HLA-C groups 1 and 2
# see http://www.ufrgs.br/imunovet/molecular_immunology/hla.html for additional details
hlaCgrp <- read.csv('data/hlaCgrp.csv', comment.char = '#', stringsAsFactors = FALSE,
na.strings = '')
save(hlaCgrp, file = 'HLA/data/hlaCgrp.RData')