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R/mbmixture is an R package for evaluating whether a microbiome sample is the mixture of two source samples. We are thinking of shotgun sequencing data on the microbiome sample plus dense SNP genotype data on the two potential source samples. We assume that the data has been reduced to a three-dimensional array of read counts: the 3 possible SNP genotypes for the first sample × the 3 possible SNP genotypes of the second sample × the 2 possible SNP alleles on the reads.
We fit a model with contaminant probability p = proportion of the microbiome sample coming from the second sample and e = rate of sequencing errors.
You can install R/mbmixture from CRAN:
install.packages("mbmixture")A vignette describing the use of the package is available on the web. Or
view it from within R by loading the package and then using the
vignette() function.
library(mbmixture)
vignette("mbmixture", package="mbmixture")To cite R/mbmixture in publications use:
Licensed under the MIT license. (More information here.)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.