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
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.
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"
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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