calculateHamming: Calculate Hamming distance between all samples

In NCBI-Hackathons/HLAClustRView: HLA typing clustering and visualization based on specific similarity metrics

Description

Takes an object containing HLA typing information for all samples and computes the Hamming distance for each pair of samples.

Usage

calculateHamming(hla_data)

Arguments

hla_data

a list of class HLADataset containing a tibble object with the HLA typing information for all samples. At least 2 samples must be present be able to calculate the metric.

Details

The Hamming distance is given by min(s1A1 != s2A1 + s1A2 != s2A2, s1A1 != s2A2 + s1A2 != s2A1) where s1 and s2 are two samples and A1 and A2 are there alleles.

Value

a list of class HLAMetric containing the following elements:

• metric a character string containing the name of the metric "Hamming Distance".

• dist a matrix that contains the Hamming distance between samples.

Author(s)

Santiago Medina, Nissim Ranade

Examples

## Load example dataset
data(demoHLADataset)

## Calculate Hamming distance metric
calculateHamming(demoHLADataset)

NCBI-Hackathons/HLAClustRView documentation built on Nov. 22, 2019, 6:11 a.m.