gtf_table.HLA: Class: gtf_tbl

In gschofl/HLAsim: Simulate allelic dropouts in HLA data

Description

Constructor for <gtf_tbl> objects. Calculates observed and expected genotype frequencies.

Usage

## S3 method for class 'HLA'
gtf_table(x)

Arguments

x	A <HLA> object.

Value

A table with the fields:

• "genotype": Key. The genotype in the format "A1/A2".

• "pexp": Expected genotype frequencies.

• "pobs": Observed genotype frequencies.

• "log_pexp": Log of expected genotype frequenciies.

• "log_pobs": Log of expected genotype frequenciies.

• "nexp": Expected number of samples for a genotype.

• "nobs": Observed number of samples for a genotype.

• "chisq": χ^2-value describing the difference between expected and observed genotype frequency.

• "log_fold_diff": Log-fold diffence between expected and observed genotype frequency.

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"]

## Remove low-resolution four-digit codes
dpb1.de <- dpb1.de[allele1 %ni% dpb1_four_digit_codes | allele2 %ni% dpb1_four_digit_codes]

## Remove cases of unknown alleles
dpb1.de <- dpb1.de[field2(allele1) != "XXX" | field2(allele2) != "XXX"]
dpb1.de <- dpb1.de[toupper(allele1) != "NEW" | toupper(allele2) != "NEW"]

## Calculate observed and expected genotype frequencies
gtf_table(dpb1.de)

## End(Not run)

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