HLA: Genotyping data generated at DKMS Life Science Lab.

In gschofl/HLAsim: Simulate allelic dropouts in HLA data

Description

An R6 reference class holding genotyping results for any of the six HLA genes routinely typed at DKMS LSL.

THIS FUNCTION REQURIES ACCESS TO INTERNAL DATABASES AT DKMS LSL.

Use the prepackaged datasets (geno_data) instead.

Usage

HLA(gene = NULL, from = NULL, to = NULL)

Arguments

gene	Fetch alleles for one of "A", "C", "B", "DRB1", "DQB1", "DPB1".
from	Start query at DD/MM/YYYY.
to	End query at DD/MM/YYYY.

Value

A <HLA> object containing a table with the following fields:

lims_donor_id

Unique sample tracking ID.

provenance

One of DE, PL, or UK.

allele1

First allele.

allele2

Other allele.

genotype

The genotype in the format "allele1/allele2", where the alleles are alphabetically ordered.

zygosity

One of homozygous or heterozygous

Examples

## Not run: 
dpb1 <- HLA("DPB1", "01/01/2014", "23/04/2015")

# restrict the sample to a country of origin
dpb1.de <- dpb1[provenance == "DE"]

# access the data table
dpb1.de.tbl <- dpb1.de$get_table()

# calculate allele frequencies
dpb1.de.af <- dpb1.de$allele_frequency()

# calculate genotype frequencies
dpb1.de.gf <- dpb1.de$genotype_frequency()

## End(Not run)

gschofl/HLAsim documentation built on May 17, 2019, 8:51 a.m.