geno_table: Class: geno_table

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

Description

Constructor function for a <geno_table> object. Created by the factory function make_genotype_sampler.

Usage

geno_table(conc, n, bin_size)

Details

A function that takes a vector of DNA concentrations to draw n random genotypes based on observed genotype frequencies and randomly attributes DNA concentrations to these genotypes.

Value

A <geno_table> object with the slots:

• "samples": table with the fields:

  • "genotype": The original genotype in format: “03:FYKD/04:ADCGE”.

  • "zygosity": One of ‘heterozygous’ or ‘homozygous’.

  • "conc": Randomly attributed DNA concentrations.

  • "bins": Intervals of DNA concentrations used to attribute concentration-dependent errors.

  • "idx": key; A running index.

• "errors": table with the fields:

  • "genotype": The genotype after error injection.

  • "zygosity": The zygosity after error injection.

  • "idx": key; A running index.

and the attributes:

• "penv": The enclosing environment of the <geno_table> constructor containing memoised mapping and remapping functions created by make_mapper and a table of observed and expected genotype frequencies generated by gtf_table.

• "breaks": The cut points used to slice up the DNA concentration.

Examples

## Not run: 
data(dpb1)
dpb1.pl <- dpb1[provenance == "PL"]

## Generate a distribution of DNA concentrations
conc <- sample_dna_concentration(dpb1.pl, n = 1000, ncores = 8)

## Generate a sampling function
data(dpb1_eag1412)
geno_table <- make_genotype_sampler(dpb1.pl, dpb1_eag1412)

## Access mapping and remapping functions as well as genotype frequencies
mapper(geno_table)
remapper(geno_table)
gtf_table(genotable)

## Sample genotypes
n <- 10000
bin_size <- 3
ans <- geno_table(conc, n, bin_size)
ans

summary(ans)
samples(ans)

## End(Not run)

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