map_genotype_frequencies: Map observed/expected genotype frequencies to sampled...

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

Description

Map observed/expected genotype frequencies to sampled genotypes

Usage

map_genotype_frequencies(x)

Arguments

x	Sample returned by inject_errors.

Value

A gtf_tbl object that can be used as a training/test data set with the slots:

• "Class": Has an error been injected in the EAGs of a sample (“event”, E), or not, (“nonevent”, N).

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

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

• "conc": Randomly attributed DNA concentrations.

• "pexp": The expected genotype frequency.

• "pobs": The observed genotype frequency.

• "log_pexp": The log of the expected genotype frequency.

• "log_pobs": The log of the observed genotype frequency.

• "log_fold_diff": The log-fold difference between observed and expected genotype frequency.

and the attributes:

• "penv": The enclosing environment of the <geno_table> constructor containing memoised mapping and remapping functions created by make_mapper, as well as genotype frequencies calculated by gtf.

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

See Also

Other simulation.functions: inject_errors, make_genotype_sampler

Examples

## Not run: 
## Extract HLA-DPB1 genotype frequencies
dpb1 <- HLA("DPB1", "01/01/2014", "23/03/2015")

## Restrict the data to the German sample
dpb1.de <- dpb1[provenance == "DE"]

## Generate an EAG table
dpb1_eag1412 <- eag_table(gene = "DPB1", nextype_basis_id = "1412")

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

## Generate a sampling function
sample_dpb1_de <- make_genotype_sampler(dpb1.de, dpb1_eag1412)

## Load precomputed DNA-concentration-dependent error distribution for HLA-A
data(cdfA)

## Sample genotypes
n <- 10000
bin_size <- 3
perr <- 0.01
odds <- 0.25
ans <- sample_dpb1_de(conc, n, bin_size) %>%
  inject_errors(cdfA, perr, odds) %>%
  map_genotype_frequencies()
ans

## End(Not run)

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