lookup_list: Class: lookup_list

In DKMS-LSL/HLAsim: Simulate allelic dropouts in HLA data

Description

Constructor for a <lookup_list> object.

Usage

lookup_list(alleles, eag)

Arguments

alleles	A character vector of alleles.
eag	EAG alleles <eag_tbl>.

Details

Inherits from <list>.

Value

A list with the elements:

e2_tbl

A mapping of rep_allele <-> eag_alllele <-> eag_num for exon 2

e3_tbl

A mapping of rep_allele <-> eag_alllele <-> eag_num for exon 2

jkr_tbl

A table of exon 3 joker alleles

prt_tbl

A mapping table with partials

ntbl2

2-field NMDP-code lookup

ntbl4

4-field NMDP-code lookup

gtbl

G-code lookup

and the attributes:

• nextype_basis_id

• gene

Examples

## Not run: 
library("HLA")

## get a vector of reported DPB1 alleles
dpb1 <- HLA::HLA("DPB1")
alleles <- HLA::get_table(dpb1)[, .(allele1, allele2)]
alleles <- sort(unique(c(alleles[, allele1], alleles[, allele2])))
alleles <- alleles[-grep("(:XXX|NEW)", alleles)]

## get an EAG table for DPB1 and a NeXtype Basis ID
eag <- eag_table("DPB1", "1267")

lookup <- lookup_list(alleles, eag)

## End(Not run)

DKMS-LSL/HLAsim documentation built on May 6, 2019, 1:17 p.m.