R package for evaluating a microbiome sample as a potential mixture
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
R
data
docs
inst/scripts
man
tests
vignettes
.Rbuildignore
.travis.yml
DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS.md
README.md

README.md

R/mbmixture

Build Status

Karl W Broman


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.


Installation

You can install R/mbmixture from its GitHub repository. You first need to install the devtools package.

install.packages("devtools")

Then install R/mbmixture using the install_github function in the devtools package. (With build_vignettes=TRUE, the vignette will be built and installed.)

library(devtools)
install_github("kbroman/mbmixture", build_vignettes=TRUE)

Vignette

A vignette describing the use of the package is available on the web. Or view it from within R by load the package and then using the vignette() function.

library(mbmixture)
vignette("mbmixture", package="mbmixture")

License

Licensed under the MIT license. (More information here.)