HLADiversityScore: Method to calculate distance between HLA alleles using...

In rbentham/HLAdivR: Calculate diversity scores between HLA class I alleles

Method to calculate distance between HLA alleles using different techniques

Description

These functions calculate the HLA diversity between alleles using several alternative methods.

Usage

HLADiversityScore(
  hla.1,
  hla.2,
  diversity.measure = "grantham",
  exons23 = TRUE,
  protdist.path = NULL
)

Arguments

hla.1	HLA allele in format A*01:01
hla.2	HLA allele in format A*01:01
diversity.measure	One of 'grantham', 'sandberg', 'pdist', 'PAM' or 'JTT'.
exons23	Logical of whether to only calculate the diversity of exons 2 and 3 the protein binding region of the HLA alleles.
protdist.path	Path to protdist app from phylip e.g. '~/Documents/Programs/phylip-3.695/exe/protdist.app/Contents/MacOS'

Value

HLA diversity metric

rbentham/HLAdivR documentation built on May 15, 2023, 1:30 p.m.