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.
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
