HLADiversity R Package

The goal of HLADiversity is to estimate the distinctiveness of HLA alleles.

• The package does the following:
  • calculates HLA allele frequency
  • plots HLA allele frequency
  • plots HLA allele count
  • compares the frequency of a target dataset to a reference population
  • plots the diversity of HLA alleles.

Data Format

The input data has to be a HLA PED file in tsv format. The columns of the HLA PED file should be in the format shown below.

• HLA class I and II alleles (A, B, C, DQA1, DQB1, DRB1, DPA1, DPB1)
• HLA allele column name separator is "."
• Include population column

A.1	A.2	B.1	B.2	C.1	C.2	DQA1.1	DQA1.2	DQB1.1	DQB1.2	DRB1.1	DRB1.2	DPA1.1	DPA1.2	DPB1.1	DPB1.2
A*30:02	A*32:01	B*42:01	B*44:03	C*04:01	C*17:01	DQA1*02:01	DQA1*04:01	DQB1*02:01	DQB1*04:02	DRB1*03:02	DRB1*07:01	DPA1*01:03	DPA1*03:03	DPB1*04:01	DPB1*04:02
A*02:03	A*33:03	B*38:02	B*58:01	C*03:02	C*07:02	DQA1*01:02	DQA1*03:01	DQB1*03:02	DQB1*06:09	DRB1*04:03	DRB1*13:02	DPA1*01:03	DPA1*02:02	DPB1*04:02	DPB1*394:01

If your HLA PED file does not have a population column, create one with the name of the dataset. For example:

hped$Population <- "1KG"

Installation

You can install the development version of HLADiversity from GitHub with:

devtools::install_github("yang-luo-lab/HLADiversity")

Running the functions

• The example datasets are derived from the 1000 Genomes (reference) and GGVP (target) datasets: https://www.internationalgenome.org/

Load Library

library(HLADiversity)

Function 1: Calculate HLA allele frequency

head(calculate_HLA_frequency(reference))
#> Loading required package: pacman
#>    allele        freq count
#> 1 A*30:02 0.028009839  1207
#> 2 A*02:03 0.002784740   120
#> 3 A*02:01 0.200106748  8623
#> 4 A*01:01 0.093451221  4027
#> 5 A*24:02 0.081917757  3530
#> 6 A*02:07 0.006312076   272

Function 2: Plot HLA allele frequecies

Plot_HLA_allele_frequency(target, minFreq = 0.05)

Function 3: Plot HLA allele counts

Plot_HLA_allele_count(reference)
#> Warning: Expected 2 pieces. Additional pieces discarded in 1 rows [481].
#> Warning: Expected 2 pieces. Missing pieces filled with `NA` in 1 rows [757].

Function 4: Compare frequency of target to reference

Plot_HLA_target_vs_ref(target, reference)
#> `geom_smooth()` using formula = 'y ~ x'

Function 5: Plot HLA allele diversity

plot_HLA_Diversity(reference, gene = "A", ntop = 5)
#> Warning: Expected 2 pieces. Additional pieces discarded in 1 rows [1201].
#> Warning: Expected 2 pieces. Missing pieces filled with `NA` in 1 rows [1].
#> Warning: Expected 2 pieces. Additional pieces discarded in 1 rows [1200].

Help

Find a description of each function and how to run it by invoking a question mark before the function in R console.

?calculate_HLA_frequency