HLADiversity/README.Rmd at main · fmobegi/HLADiversity · GitHub

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---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# HLADiversity

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

## Input file format


## Installation

You can install the development version of HLADiversity from [GitHub](https://github.com) with:

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

## Example

This is a basic example of how to run the functions:

```{r }
library(HLADiversity)
```

```{r }
head(calculate_HLA_frequency(reference))
```

```{r }
Plot_HLA_allele_frequency(target, minFreq = 0.05)
```

```{r }
Plot_HLA_allele_count(reference)
```

```{r }
Plot_HLA_target_vs_ref(target, reference)
```

```{r}
plot_HLA_Diversity(reference, gene = "A", ntop = 5)
```