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Infer transmission clusters from SNP and timing data
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README.md

transcluster

Introduction

This is transcluster, a package for inferring and viewing transmission clusters from sequence alignments and sample dates.

The package takes two kinds of input data

  • SNP distance matrix
  • Sample dates

which can be provided directly or from fasta and csv files respectively.

There is a simple starter vignette in the vignettes folder.

A formal description of the methods is written up in Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions, by James Stimson, Jennifer Leigh Gardy, Barun Mathema, Valeriu Crudu, Theodore Cohen, and Caroline Colijn.

Installation

You can install transcluster in R using the following command:

devtools::install_github("JamesStimson/transcluster", build_vignettes = TRUE)

There are some example input files that come with the installation. To find out where they are on your system, use system.file() like this:

system.file("extdata", "bc_snp_matrix_R.csv", package = "transcluster", mustWork = TRUE)

You will see something like this in response:

[1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/transcluster/extdata/bc_snp_matrix_R.csv"

Getting help

To view the vignette once installed, run

vignette("how-to-guide", package = "transcluster")

Alternatively, you can run the R markdown vignettes/how-to-guide.Rmd yourself.

If you need further assistance using transcluster, you can get in touch by emailing

james.stimson16@imperial.ac.uk
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