EvalAlleleMism: Evaluate mismatched alleles

Description Usage Arguments Value Examples

View source: R/allele-eval-mism.R

Description

Compare donor and recipient HLA(Human Leukocyte Antigen) typing data to determine mismatched alleles. Input data can be high or low resolution, mismatch is evaluated at the allele level.

Usage

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EvalAlleleMism(don_1, don_2, recip_1, recip_2, hmz_cnt = 1)

Arguments

don_1

Donor's alpha1 domain.

don_2

Donor's alpha2 or beta1 domain.

recip_1

Recipient's alpha1 domain.

recip_2

Recipient's alpha2 or beta1 domain.

hmz_cnt

Use hmz_cnt to determine how mismatch at homozygous alleles should be handled. By default, a mismatch at a homozygous allele is considered a single mismatch. Set hmz_cnt = 2 to count homozygous mismatches as double.

Value

A data frame of original input columns followed by mism_cnt of each donor/recipient pair.

Examples

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dat <- read.csv(system.file("extdata/example", "HLA_Clean_test.csv", package = "hlaR"))
re <- EvalAlleleMism(dat$donor_a1, dat$donor_a2, dat$recipient_a1, dat$recipient_a2, hmz_cnt = 2)

hlaR documentation built on Sept. 28, 2021, 1:06 a.m.